User:Adam Meade/Sandbox 1: Difference between revisions

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'''''Iron Response Regulator (Irr)'''''

----

=Background Information=

Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules. Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis. Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in ''Rhodobacter sphaeroides'' form a cluster in the order ''fecI-fecR-fecABCDE'', encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter. In ''Escherichia coli'', ''fecI'' transcription is regulated by Fur in response to iron availability; in ''Bradyrhizobium japonicum'', as well as ''R. sphaeroides'', which both lack Fur, ''fecI'' transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins. <ref>Hamza I, S. Chauhan, R. Hassett, M. R. O'Brian, 1998. The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.. Journal of Biological Chemistry 34:21669-74.</ref>

=Irr and Other Iron-Regulating Proteins=

Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place. In the case of ''B. japonicum'', which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.<ref>Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>

=Function of Irr=

Irr behaves differently than other regulatory proteins. To prevent the accumulation of toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced. <ref>Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>

Irr accumulates in cells under iron limitation, with very low levels of Irr being present in iron-replete cells. This is a distinction when compared to other Fur family proteins because it functions in the absence of the regulatory metal, whereas the other members require direct metal-binding for the protein to be activated. <ref>Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>

=Phylogenetic Tree=

http://consurf.tau.ac.il/results/1240766462/treeView.html

=Chemical and Physical Properties of Irr=

Molecular weight: 18338.8 Da

Theoretical pI: 6.03

{| border="1"

|+ Amino Acid Composition

! Amino Acid !! Number present !! Percentage of total present

|-

! align="center"| Ala (A)

| align="center"| 15 || align="center"| 9.2%

|-

! align="center"| Arg (R)

| align="center"| 10 || align="center"| 6.1%

|-

! align="center"| Asn (N)

| align="center"| 6 || align="center"| 3.7%

|-

! align="center"| Asp (D)

| align="center"| 10 || align="center"| 6.1%

|-

! align="center"| Cys (C)

| align="center"| 1 || align="center"| 0.6%

|-

! align="center"| Gln (Q)

| align="center"| 5 || align="center"| 3.1%

|-

! align="center"| Glu (E)

| align="center"| 11 || align="center"| 6.7%

|-

! align="center"| Gly (G)

| align="center"| 9 || align="center"| 5.5%

|-

! align="center"| His (H)

| align="center"| 10 || align="center"| 6.1%

|-

! align="center"| Ile (I)

| align="center"| 3 || align="center"| 1.8%

|-

! align="center"| Leu (L)

| align="center"| 21 || align="center"| 12.9%

|-

! align="center"| Lys (K)

| align="center"| 6 || align="center"| 3.7%

|-

! align="center"| Met (M)

| align="center"| 6 || align="center"| 3.7%

|-

! align="center"| Phe (F)

| align="center"| 2 || align="center"| 1.2%

|-

! align="center"| Pro (P)

| align="center"| 8 || align="center"| 4.9%

|-

! align="center"| Ser (S)

| align="center"| 7 || align="center"| 4.3%

|-

! align="center"| Thr (T)

| align="center"| 13 || align="center"| 8.0%

|-

! align="center"| Trp (W)

| align="center"| 2 || align="center"| 1.2%

|-

! align="center"| Tyr (Y)

| align="center"| 6 || align="center"| 3.7%

|-

! align="center"| Val (V)

| align="center"| 12 || align="center"| 7.4%

|-

! align="center"| Pyl (O)

| align="center"| 0 || align="center"| 0.0%

|-

! align="center"| Sec (U)

| align="center"| 0 || align="center"| 0.0%

|}

=Evolution of Irr/Fur=

Amino Acid Conservation Scores

----

~~'''Background Information'''~~

The following are scores on how well conserved the amino acids are in relation to proteins with a similar structure to Irr. This could potentially show us where Irr evolved from/what Irr will evolve into.

- POS: The position of the AA in the SEQRES derived sequence.

Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules. Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis. Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in ''Rhodobacter sphaeroides'' form a cluster in the order ''fecI-fecR-fecABCDE'', encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter. In ''Escherichia coli'', ''fecI'' transcription is regulated by Fur in response to iron availability; in ''Bradyrhizobium japonicum'', as well as ''R. sphaeroides'', which both lack Fur, ''fecI'' transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins. <ref>1) Hamza I, S. Chauhan, R. Hassett, MR O'Brian, 1998. The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.. Journal of Biological Chemistry 34:21669-74.~~</ref>~~

- SEQ: The SEQRES derived sequence in one letter code.

- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).

- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.

~~'''Irr and Other Iron-Regulating Proteins'''~~

Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place. In the case of ''B. japonicum'', which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.<ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>

POS SEQ COLOR RESIDUE VARIETY

(normalized)

1 D 9 D

2 V 2* F,N,V,Y

3 N 6 A,N,S,T

4 E 3* E,G,K,Q,S,T

5 M 3* A,E,I,L,M,Q,T

6 L 9 L

7 Q 7 K,Q,R

8 S 1 D,E,K,N,Q,R,S,T

9 A 5 A,G,I,M,N,S,T,V

10 G 8 D,G

11 L 8 I,L,V

12 R 8 K,R

13 P 4 A,I,P,V,Y

14 T 9 T

15 R 3* E,F,G,K,L,P,R,V

16 Q 8 P,Q

17 R 9 R

18 M 3* E,H,I,L,M,Q,V

19 A 8 A,K,T,V

20 L 7 I,L,V

21 G 6 G,I,L,M

22 W 1 A,D,E,K,N,Q,R,W

23 L 1 A,F,I,L,M,T,V,Y

24 L 7 F,L,M,V

25 F 1 D,E,F,I,K,N,Q,R,V,Y

26 G 1 A,E,G,H,K,N,Q,S,T

27 K 3* A,E,H,K,P,S,T

28 G 1 A,D,E,G,H,K,M,P,R

29 A 1 A,C,E,G,L,M,N,Q,S,T

30 R 1 E,H,Q,R

31 H 9 H

32 L 3* A,F,I,L,M,P,V,Y

33 T 8 D,E,S,T

34 A 9 A,P,T

35 E 8 D,E

36 M 3* A,D,E,H,M,S,T

37 L 5 C,I,L,V

38 Y 7 F,I,Y

39 E 5 E,G,K,M,N,Q,R

40 E 1 A,E,H,I,K,L,R

41 A 6 A,F,I,L,V

42 T 2 A,E,I,L,M,R,S,T

43 L 1 A,D,E,F,G,L,N,P,S,V

44 A 1 A,D,E,I,K,L,M,P,Q,R,S

45 K 1 D,F,G,H,K,L,N,S

46 V 3* C,E,L,M,P,S,V

47 P 4 D,E,N,P

48 V 7 I,M,V

49 S 9 G,S

50 L 5 H,I,L,R,V

51 A 9 A,Q,S

52 T 9 A,T

53 V 8 I,V

54 Y 9 Y

55 N 8 D,N,R

56 T 8 N,T,V,X

57 L 9 L

58 N 7 H,K,N,R,T

59 Q 7 A,L,Q,V

60 L 7 F,L,M

61 T 5 A,D,E,K,R,T

62 D 4 A,D,E,Q,R,S

63 A 7 A,I,M,S,V

64 G 8 E,G,H

65 L 6 I,L,M

66 L 7 L,V

67 R 4 I,K,L,Q,R,S,T,V

68 Q 6 E,K,Q,R,S

69 V 5 H,I,L,N,S,V

70 S 5 D,H,N,P,Q,S,T

71 V 5 F,L,P,V,Y

72 D 2 A,D,E,G,S,T

73 G 5 D,E,G,S,T

74 T 5 A,D,G,N,S,T

75 K 5 G,H,K,S,V

76 T 6 A,K,S,T

77 Y 6 H,I,K,R,V,Y

78 F 6 F,Y

79 D 8 D,E

80 T 6 F,L,S,T

81 N 3 A,D,N,R,S,T,V

82 V 4* Q,V

83 T 1 D,E,K,N,P,Q,T,V

84 T 1 D,G,K,L,N,Q,S,T

85 H 1 D,E,G,H,K,P,S

86 H 8 D,E,H,N

87 H 9 H

88 Y 8 D,H,Y

89 Y 9 H,Y

90 L 2 A,I,L,M,V

91 E 1 E,K,L,M,T,V

92 N 2* D,E,K,N,Q,V

93 S 7 C,S,T

94 H 5 G,H,N,S

95 E 6 E,K,T

96 L 8 I,L,V

97 V 6 F,I,T,V

98 D 8 D,E

99 I 8 F,I

100 E 1 E,H,K,M,Q,S,T

101 D 6 D,N,S,Y

102 P 6 A,E,N,P

103 H 1 D,E,G,H,I,Q,V

104 L 8 I,L

105 A 3* A,K,Q

106 L 5* L,R

107 S 7 Q,S

108 K 3* D,K,R

109 M 4* E,K,M

110 P 7 I,P

111 E 4* A,E,S,V

112 V 2* A,E,R,V

113 P 3* E,K,P,Q

114 E 1 E,H,N,R,Y

115 G 7 G,N

116 Y 2 F,I,V,Y

117 E 5* E,R

118 I 6* I,L

119 A 6* A,V

120 R 4* D,R

121 I 4* H,I

122 D 6* D,N

123 M 6* L,M

124 V 8* V

125 V 5* L,V

126 R 4* R,Y

127 L 6* L,V

128 R 8* R

129 K 8* K

130 K 8* K

131 R 6* K,R

~~'''Function of Irr'''~~

Irr behaves differently than other regulatory proteins. It functions as coordinating the heme biosynthetic pathway, which ends with the insertion of Fe2+ into a protoporphyrin ring to produce protoheme. It also controls the pathway by monitoring iron availability to prevent the accumulation of ~~toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced. <ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by~~ the ~~iron response regulator (~~Irr~~) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>~~

=Structure of the Proposed Irr Protein=

Irr ~~accumulates in cells under iron limitation, with very low levels of Irr being present in iron-replete cells~~. ~~This is a distinction when compared to other Fur family proteins because it functions in the absence~~ of the regulatory metal, whereas the other members require direct metal-binding for the protein to be activated. <ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein ~~in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.<~~/~~ref~~>

<scene name='User:Adam_Meade/Sandbox_1/Secondary_structure_-_irr/1'>Secondary Structure</scene>

<scene name='User:Adam_Meade/Sandbox_1/Polar_regions/2'>Polar/Hydrophobic Regions</scene>

<scene name='User:Adam_Meade/Sandbox_1/N_to_c_rainbow/1'>Amino terminus to carboxy terminus</scene>

~~'''Structure of the Proposed Irr Protein'''<applet load='Irr.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed Irr protein'/>~~

The amino acid sequence used to derive the structure shown is as follows:

1 msentaphhd ddvhaaalls grqpaltgcp whdvnemlqs aglrptrqrm algwllfgkg

Line 56:

Line 301:

=References=

HOW WAS THE ANIMATED IMAGE GENERATED?

1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html

2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.

3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.

4. On "advanced structural annotation" section select 'docking models in Capri format'.

5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.

HOW WAS THE JMOL IMAGE GENERATED?

1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.

2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.

~~==References==~~

3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.

~~1) Hamza I, S~~. ~~Chauhan, R~~. ~~Hassett, M~~. ~~R. O'Brian, 1998. The bacterial irr protein is required for coordination of heme biosynthesis with iron availability~~.</~~u>. Journal of Biological Chemistry 34~~:~~21669-74~~.

~~2) Small, S~~. ~~K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation~~ by the ~~iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97~~.

4. You can edit your protein by using the scene authoring tools after loading the applet.

@@ Line 1: / Line 1: @@
 '''''Iron Response Regulator (Irr)'''''
+----
+=Background Information=
+Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules.  Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis.  Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in ''Rhodobacter sphaeroides'' form a cluster in the order ''fecI-fecR-fecABCDE'', encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter.  In ''Escherichia coli'', ''fecI'' transcription is regulated by Fur in response to iron availability; in ''Bradyrhizobium japonicum'', as well as ''R. sphaeroides'', which both lack Fur, ''fecI'' transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins.  <ref>Hamza I, S. Chauhan, R. Hassett, M. R. O'Brian, 1998.  <u>The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.</u>.  Journal of Biological Chemistry 34:21669-74.</ref>
+=Irr and Other Iron-Regulating Proteins=
+Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place.  In the case of ''B. japonicum'', which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.<ref>Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
+=Function of Irr=
+Irr behaves differently than other regulatory proteins.  To prevent the accumulation of toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced.  <ref>Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
+Irr accumulates in cells under iron limitation, with very low levels of Irr being present in iron-replete cells.  This is a distinction when compared to other Fur family proteins because it functions in the absence of the regulatory metal, whereas the other members require direct metal-binding for the protein to be activated.  <ref>Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
+=Phylogenetic Tree=
+http://consurf.tau.ac.il/results/1240766462/treeView.html
+=Chemical and Physical Properties of Irr=
+Molecular weight: 18338.8 Da
+Theoretical pI: 6.03
+{| border="1"
+|+ Amino Acid Composition
+! Amino Acid !! Number present !! Percentage of total present
+|-
+! align="center"| Ala (A)
+| align="center"| 15 || align="center"| 9.2%
+|-
+! align="center"| Arg (R)
+| align="center"| 10 || align="center"| 6.1%
+|-
+! align="center"| Asn (N)
+| align="center"| 6 || align="center"| 3.7%
+|-
+! align="center"| Asp (D)
+| align="center"| 10 || align="center"| 6.1%
+|-
+! align="center"| Cys (C)
+| align="center"| 1 || align="center"| 0.6%
+|-
+! align="center"| Gln (Q)
+| align="center"| 5 || align="center"| 3.1%
+|-
+! align="center"| Glu (E)
+| align="center"| 11 || align="center"| 6.7%
+|-
+! align="center"| Gly (G)
+| align="center"| 9 || align="center"| 5.5%
+|-
+! align="center"| His (H)
+| align="center"| 10 || align="center"| 6.1%
+|-
+! align="center"| Ile (I)
+| align="center"| 3 || align="center"| 1.8%
+|-
+! align="center"| Leu (L)
+| align="center"| 21 || align="center"| 12.9%
+|-
+! align="center"| Lys (K)
+| align="center"| 6 || align="center"| 3.7%
+|-
+! align="center"| Met (M)
+| align="center"| 6 || align="center"| 3.7%
+|-
+! align="center"| Phe (F)
+| align="center"| 2 || align="center"| 1.2%
+|-
+! align="center"| Pro (P)
+| align="center"| 8 || align="center"| 4.9%
+|-
+! align="center"| Ser (S)
+| align="center"| 7 || align="center"| 4.3%
+|-
+! align="center"| Thr (T)
+| align="center"| 13 || align="center"| 8.0%
+|-
+! align="center"| Trp (W)
+| align="center"| 2 || align="center"| 1.2%
+|-
+! align="center"| Tyr (Y)
+| align="center"| 6 || align="center"| 3.7%
+|-
+! align="center"| Val (V)
+| align="center"| 12 || align="center"| 7.4%
+|-
+! align="center"| Pyl (O)
+| align="center"| 0 || align="center"| 0.0%
+|-
+! align="center"| Sec (U)
+| align="center"| 0 || align="center"| 0.0%
+|}
+=Evolution of Irr/Fur=
+Amino Acid Conservation Scores
 ----
-'''Background Information'''
+The following are scores on how well conserved the amino acids are in relation to proteins with a similar structure to Irr.  This could potentially show us where Irr evolved from/what Irr will evolve into.
+- POS: The position of the AA in the SEQRES derived sequence.
-Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules.  Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis.  Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in ''Rhodobacter sphaeroides'' form a cluster in the order ''fecI-fecR-fecABCDE'', encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter.  In ''Escherichia coli'', ''fecI'' transcription is regulated by Fur in response to iron availability; in ''Bradyrhizobium japonicum'', as well as ''R. sphaeroides'', which both lack Fur, ''fecI'' transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins.  <ref>1) Hamza I, S. Chauhan, R. Hassett, MR O'Brian, 1998.  <u>The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.</u>.  Journal of Biological Chemistry 34:21669-74.</ref>
+- SEQ: The SEQRES derived sequence in one letter code.
+- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
+- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
-'''Irr and Other Iron-Regulating Proteins'''
-Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place.  In the case of ''B. japonicum'', which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.<ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
+ POS	 SEQ	    COLOR	RESIDUE VARIETY
+    	    	        	(normalized)
+	   D	      9	         D
+	   V	      2*         F,N,V,Y
+	   N	      6	         A,N,S,T
+	   E	      3*	 E,G,K,Q,S,T
+	   M	      3*	 A,E,I,L,M,Q,T
+	   L	      9	         L
+	   Q	      7          K,Q,R
+	   S	      1          D,E,K,N,Q,R,S,T
+	   A	      5	         A,G,I,M,N,S,T,V
+	   G	      8          D,G
+	   L	      8          I,L,V
+	   R	      8	         K,R
+	   P	      4          A,I,P,V,Y
+	   T	      9          T
+	   R	      3*	 E,F,G,K,L,P,R,V
+	   Q	      8	         P,Q
+	   R	      9          R
+	   M	      3*	 E,H,I,L,M,Q,V
+	   A	      8          A,K,T,V
+	   L	      7          I,L,V
+	   G	      6          G,I,L,M
+	   W	      1          A,D,E,K,N,Q,R,W
+	   L	      1          A,F,I,L,M,T,V,Y
+	   L	      7          F,L,M,V
+	   F	      1	         D,E,F,I,K,N,Q,R,V,Y
+	   G	      1	         A,E,G,H,K,N,Q,S,T
+	   K	      3*	 A,E,H,K,P,S,T
+	   G	      1	         A,D,E,G,H,K,M,P,R
+	   A	      1	         A,C,E,G,L,M,N,Q,S,T
+	   R	      1	         E,H,Q,R
+	   H	      9	         H
+	   L	      3*	 A,F,I,L,M,P,V,Y
+	   T	      8	         D,E,S,T
+	   A	      9	         A,P,T
+	   E	      8	         D,E
+	   M	      3*	 A,D,E,H,M,S,T
+	   L	      5	         C,I,L,V
+	   Y	      7	         F,I,Y
+	   E	      5	         E,G,K,M,N,Q,R
+	   E	      1	         A,E,H,I,K,L,R
+	   A	      6	         A,F,I,L,V
+	   T	      2	         A,E,I,L,M,R,S,T
+	   L	      1	         A,D,E,F,G,L,N,P,S,V
+	   A	      1	         A,D,E,I,K,L,M,P,Q,R,S
+	   K	      1	         D,F,G,H,K,L,N,S
+	   V	      3*	 C,E,L,M,P,S,V
+	   P	      4	         D,E,N,P
+	   V	      7	         I,M,V
+	   S	      9	         G,S
+	   L	      5	         H,I,L,R,V
+	   A	      9	         A,Q,S
+	   T	      9	         A,T
+	   V	      8	         I,V
+	   Y	      9	         Y
+	   N	      8	         D,N,R
+	   T	      8	         N,T,V,X
+	   L	      9	         L
+	   N	      7	         H,K,N,R,T
+	   Q	      7	         A,L,Q,V
+	   L	      7	         F,L,M
+	   T	      5	         A,D,E,K,R,T
+	   D	      4	         A,D,E,Q,R,S
+	   A	      7	         A,I,M,S,V
+	   G	      8	         E,G,H
+	   L	      6	         I,L,M
+	   L	      7	         L,V
+	   R	      4	         I,K,L,Q,R,S,T,V
+	   Q	      6	         E,K,Q,R,S
+	   V	      5	         H,I,L,N,S,V
+	   S	      5	         D,H,N,P,Q,S,T
+	   V	      5	         F,L,P,V,Y
+	   D	      2	         A,D,E,G,S,T
+	   G	      5	         D,E,G,S,T
+	   T	      5	         A,D,G,N,S,T
+	   K	      5	         G,H,K,S,V
+	   T	      6	         A,K,S,T
+	   Y	      6	         H,I,K,R,V,Y
+	   F	      6	         F,Y
+	   D	      8	         D,E
+	   T	      6	         F,L,S,T
+	   N	      3	         A,D,N,R,S,T,V
+	   V	      4*	 Q,V
+	   T	      1	         D,E,K,N,P,Q,T,V
+	   T	      1	         D,G,K,L,N,Q,S,T
+	   H	      1	         D,E,G,H,K,P,S
+	   H	      8	         D,E,H,N
+	   H	      9	         H
+	   Y	      8	         D,H,Y
+	   Y	      9          H,Y
+	   L	      2	         A,I,L,M,V
+	   E	      1	         E,K,L,M,T,V
+	   N	      2*	 D,E,K,N,Q,V
+	   S	      7	         C,S,T
+	   H	      5	         G,H,N,S
+	   E	      6	         E,K,T
+	   L	      8	         I,L,V
+	   V	      6	         F,I,T,V
+	   D	      8	         D,E
+	   I	      8	         F,I
+	   E	      1	         E,H,K,M,Q,S,T
+	   D	      6	         D,N,S,Y
+	   P	      6	         A,E,N,P
+	   H	      1	         D,E,G,H,I,Q,V
+	   L	      8	         I,L
+	   A	      3*	 A,K,Q
+	   L	      5*	 L,R
+	   S	      7	         Q,S
+	   K	      3*	 D,K,R
+	   M	      4*	 E,K,M
+	   P	      7	         I,P
+	   E	      4*	 A,E,S,V
+	   V	      2*	 A,E,R,V
+	   P	      3*	 E,K,P,Q
+	   E	      1	         E,H,N,R,Y
+	   G	      7	         G,N
+	   Y	      2	         F,I,V,Y
+	   E	      5*	 E,R
+	   I	      6*	 I,L
+	   A	      6*	 A,V
+	   R	      4*	 D,R
+	   I	      4*	 H,I
+	   D	      6*	 D,N
+	   M	      6*	 L,M
+	   V	      8*	 V
+	   V	      5*	 L,V
+	   R	      4*	 R,Y
+	   L	      6*	 L,V
+	   R	      8*	 R
+	   K	      8*	 K
+	   K	      8*	 K
+	   R	      6*	 K,R
-'''Function of Irr'''
-Irr behaves differently than other regulatory proteins.  It functions as coordinating the heme biosynthetic pathway, which ends with the insertion of Fe<sup>2+</sup> into a protoporphyrin ring to produce protoheme.  It also controls the pathway by monitoring iron availability to prevent the accumulation of toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced.  <ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
+=Structure of the Proposed Irr Protein=
-Irr accumulates in cells under iron limitation, with very low levels of Irr being present in iron-replete cells.  This is a distinction when compared to other Fur family proteins because it functions in the absence of the regulatory metal, whereas the other members require direct metal-binding for the protein to be activated.  <ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
+<applet load='Irr.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed Irr protein'/>
+<scene name='User:Adam_Meade/Sandbox_1/Secondary_structure_-_irr/1'>Secondary Structure</scene>
+<scene name='User:Adam_Meade/Sandbox_1/Polar_regions/2'>Polar/Hydrophobic Regions</scene>
+<scene name='User:Adam_Meade/Sandbox_1/N_to_c_rainbow/1'>Amino terminus to carboxy terminus</scene>
+{{Template:ColorKey_Amino2CarboxyRainbow}}
-'''Structure of the Proposed Irr Protein'''<applet load='Irr.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed Irr protein'/>
 The amino acid sequence used to derive the structure shown is as follows:
 msentaphhd ddvhaaalls grqpaltgcp whdvnemlqs aglrptrqrm algwllfgkg
@@ Line 56: / Line 301: @@
+=References=
+<references/>
+HOW WAS THE ANIMATED IMAGE GENERATED?
+. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
+. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.
+. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.
+. On "advanced structural annotation" section select 'docking models in Capri format'.
+. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.
+HOW WAS THE JMOL IMAGE GENERATED?
+. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.
+. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.
-==References==
+. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.
-) Hamza I, S. Chauhan, R. Hassett, M. R. O'Brian, 1998.  <u>The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.</u>.  Journal of Biological Chemistry 34:21669-74.
-) Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.
+. You can edit your protein by using the scene authoring tools after loading the applet.