Proteopedia

User:Adam Meade/Sandbox 1: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 14: Line 14:


=Function of Irr=
=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>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 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>
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




Line 110: Line 114:


- SEQ: The SEQRES derived sequence in one letter code.
- SEQ: The SEQRES derived sequence in one letter code.
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
- SCORE: The normalized conservation scores.


- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.


- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
Line 178: Line 172:
   48   V       7         I,M,V             
   48   V       7         I,M,V             
   49   S       9         G,S               
   49   S       9         G,S               
   50   L     LEU82: -0.133   5 -0.570, 0.294     7,4   29/29 H,I,L,R,V         
   50   L       5         H,I,L,R,V         
   51   A     ALA83: -1.171   9 -1.338,-0.986     9,8   29/29 A,Q,S             
   51   A       9         A,Q,S             
   52   T     THR84: -1.376   9 -1.588,-1.223     9,9   29/29 A,T               
   52   T       9         A,T               
   53   V     VAL85: -1.007   8 -1.223,-0.859     9,8   29/29 I,V               
   53   V       8         I,V               
   54   Y     TYR86: -1.335   9 -1.588,-1.223     9,9   29/29 Y                 
   54   Y       9         Y                 
   55   N     ASN87: -1.123   8 -1.338,-0.986     9,8   29/29 D,N,R             
   55   N       8         D,N,R             
   56   T     THR88: -0.956   8 -1.223,-0.721     9,7   29/29 N,T,V,X           
   56   T       8         N,T,V,X           
   57   L     LEU89: -1.357   9 -1.588,-1.223     9,9   29/29 L                 
   57   L       9         L                 
   58   N     ASN90: -0.647   7 -0.986,-0.403     8,6   29/29 H,K,N,R,T         
   58   N       7         H,K,N,R,T         
   59   Q     GLN91: -0.558   7 -0.859,-0.210     8,6   29/29 A,L,Q,V           
   59   Q       7         A,L,Q,V           
   60   L     LEU92: -0.570   7 -0.986,-0.210     8,6   29/29 F,L,M             
   60   L       7         F,L,M             
   61   T     THR93: -0.099   5 -0.570, 0.294     7,4   29/29 A,D,E,K,R,T       
   61   T       5         A,D,E,K,R,T       
   62   D     ASP94: 0.354   4 -0.210, 0.661     6,3   29/29 A,D,E,Q,R,S       
   62   D       4         A,D,E,Q,R,S       
   63   A     ALA95: -0.757   7 -1.107,-0.570     8,7   29/29 A,I,M,S,V         
   63   A       7         A,I,M,S,V         
   64   G     GLY96: -0.841   8 -1.223,-0.570     9,7   29/29 E,G,H             
   64   G       8         E,G,H             
   65   L     LEU97: -0.306   6 -0.721, 0.016     7,5   29/29 I,L,M             
   65   L       6         I,L,M             
   66   L     LEU98: -0.712   7 -0.986,-0.403     8,6   29/29 L,V               
   66   L       7         L,V               
   67   R     ARG99: 0.384   4 -0.210, 0.661     6,3   29/29 I,K,L,Q,R,S,T,V   
   67   R       4         I,K,L,Q,R,S,T,V   
   68   Q   GLN100: -0.238   6 -0.570, 0.016     7,5   29/29 E,K,Q,R,S         
   68   Q       6         E,K,Q,R,S         
   69   V   VAL101: -0.147   5 -0.570, 0.294     7,4   29/29 H,I,L,N,S,V       
   69   V       5         H,I,L,N,S,V       
   70   S   SER102: 0.078   5 -0.403, 0.294     6,4   29/29 D,H,N,P,Q,S,T     
   70   S       5         D,H,N,P,Q,S,T     
   71   V   VAL103: 0.145   5 -0.403, 0.661     6,3   29/29 F,L,P,V,Y         
   71   V       5         F,L,P,V,Y         
   72   D   ASP104: 0.881   2 0.294, 1.214     4,1   29/29 A,D,E,G,S,T       
   72   D       2         A,D,E,G,S,T       
   73   G   GLY105: 0.110   5 -0.403, 0.661     6,3   29/29 D,E,G,S,T         
   73   G       5         D,E,G,S,T         
   74   T   THR106: -0.006   5 -0.403, 0.294     6,4   29/29 A,D,G,N,S,T       
   74   T       5         A,D,G,N,S,T       
   75   K   LYS107: 0.077   5 -0.403, 0.294     6,4   29/29 G,H,K,S,V         
   75   K       5         G,H,K,S,V         
   76   T   THR108: -0.179   6 -0.570, 0.016     7,5   29/29 A,K,S,T           
   76   T       6         A,K,S,T           
   77   Y   TYR109: -0.415   6 -0.721,-0.210     7,6   29/29 H,I,K,R,V,Y       
   77   Y       6         H,I,K,R,V,Y       
   78   F   PHE110: -0.368   6 -0.721, 0.016     7,5   29/29 F,Y               
   78   F       6         F,Y               
   79   D   ASP111: -1.082   8 -1.338,-0.859     9,8   29/29 D,E               
   79   D       8         D,E               
   80   T   THR112: -0.448   6 -0.859,-0.210     8,6   29/29 F,L,S,T           
   80   T       6         F,L,S,T           
   81   N   ASN113: 0.772   3 0.294, 1.214     4,1   29/29 A,D,N,R,S,T,V     
   81   N       3         A,D,N,R,S,T,V     
   82   V   VAL114: 0.383   4* -0.570, 1.214     7,1     2/29 Q,V               
   82   V       4* Q,V               
   83   T   THR115: 2.165   1 1.214, 2.633     1,1   23/29 D,E,K,N,P,Q,T,V   
   83   T       1         D,E,K,N,P,Q,T,V   
   84   T   THR116: 1.506   1 0.661, 2.633     3,1   29/29 D,G,K,L,N,Q,S,T   
   84   T       1         D,G,K,L,N,Q,S,T   
   85   H   HIS117: 1.472   1 0.661, 2.633     3,1   29/29 D,E,G,H,K,P,S     
   85   H       1         D,E,G,H,K,P,S     
   86   H   HIS118: -0.825   8 -1.107,-0.570     8,7   29/29 D,E,H,N           
   86   H       8         D,E,H,N           
   87   H   HIS119: -1.467   9 -1.588,-1.455     9,9   29/29 H                 
   87   H       9         H                 
   88   Y   TYR120: -0.874   8 -1.107,-0.721     8,7   29/29 D,H,Y             
   88   Y       8         D,H,Y             
   89   Y   TYR121: -1.329   9 -1.455,-1.223     9,9   29/29 H,Y               
   89   Y       9         H,Y               
   90   L   LEU122: 1.136   2 0.294, 1.214     4,1   25/29 A,I,L,M,V         
   90   L       2         A,I,L,M,V         
   91   E   GLU123: 1.417   1 0.661, 2.633     3,1   18/29 E,K,L,M,T,V       
   91   E       1         E,K,L,M,T,V       
   92   N   ASN124: 0.930   2* 0.016, 1.214     5,1   18/29 D,E,K,N,Q,V       
   92   N       2* D,E,K,N,Q,V       
   93   S   SER125: -0.572   7 -0.986,-0.210     8,6   18/29 C,S,T             
   93   S       7         C,S,T             
   94   H   HIS126: -0.108   5 -0.721, 0.294     7,4   18/29 G,H,N,S           
   94   H       5         G,H,N,S           
   95   E   GLU127: -0.355   6 -0.859, 0.016     8,5   18/29 E,K,T             
   95   E       6         E,K,T             
   96   L   LEU128: -0.913   8 -1.223,-0.721     9,7   18/29 I,L,V             
   96   L       8         I,L,V             
   97   V   VAL129: -0.280   6 -0.721, 0.016     7,5   18/29 F,I,T,V           
   97   V       6         F,I,T,V           
   98   D   ASP130: -1.063   8 -1.338,-0.859     9,8   18/29 D,E               
   98   D       8         D,E               
   99   I   ILE131: -0.905   8 -1.223,-0.721     9,7   18/29 F,I               
   99   I       8         F,I               
  100   E   GLU132: 1.739   1 1.214, 2.633     1,1   18/29 E,H,K,M,Q,S,T     
  100   E       1         E,H,K,M,Q,S,T     
  101   D   ASP133: -0.254   6 -0.721, 0.016     7,5   18/29 D,N,S,Y           
  101   D       6         D,N,S,Y           
  102   P   PRO134: -0.193   6 -0.721, 0.294     7,4   18/29 A,E,N,P           
  102   P       6         A,E,N,P           
  103   H   HIS135: 1.561   1 0.661, 2.633     3,1   16/29 D,E,G,H,I,Q,V     
  103   H       1         D,E,G,H,I,Q,V     
  104   L   LEU136: -1.023   8 -1.338,-0.859     9,8   16/29 I,L               
  104   L       8         I,L               
  105   A   ALA137: 0.666   3* -0.210, 1.214     6,1     7/29 A,K,Q             
  105   A       3* A,K,Q             
  106   L   LEU138: 0.051   5* -0.721, 0.661     7,3     7/29 L,R               
  106   L       5* L,R               
  107   S   SER139: -0.624   7 -1.107,-0.210     8,6     7/29 Q,S               
  107   S       7         Q,S               
  108   K   LYS140: 0.661   3* -0.210, 1.214     6,1     7/29 D,K,R             
  108   K       3* D,K,R             
  109   M   MET141: 0.164   4* -0.570, 0.661     7,3     7/29 E,K,M             
  109   M       4* E,K,M             
  110   P   PRO142: -0.492   7 -0.986,-0.210     8,6     7/29 I,P               
  110   P       7         I,P               
  111   E   GLU143: 0.243   4* -0.570, 0.661     7,3     7/29 A,E,S,V           
  111   E       4* A,E,S,V           
  112   V   VAL144: 0.835   2* 0.016, 1.214     5,1     7/29 A,E,R,V           
  112   V       2* A,E,R,V           
  113   P   PRO145: 0.779   3* 0.016, 1.214     5,1     7/29 E,K,P,Q           
  113   P       3* E,K,P,Q           
  114   E   GLU146: 1.555   1 0.661, 2.633     3,1     7/29 E,H,N,R,Y         
  114   E       1         E,H,N,R,Y         
  115   G   GLY147: -0.540   7 -1.107,-0.210     8,6     7/29 G,N               
  115   G       7         G,N               
  116   Y   TYR148: 1.072   2 0.294, 2.633     4,1     7/29 F,I,V,Y           
  116   Y       2         F,I,V,Y           
  117   E   GLU149: -0.017   5* -0.859, 0.661     8,3     5/29 E,R               
  117   E       5* E,R               
  118   I   ILE150: -0.332   6* -0.986, 0.016     8,5     5/29 I,L               
  118   I       6* I,L               
  119   A   ALA151: -0.318   6* -0.986, 0.016     8,5     3/29 A,V               
  119   A       6* A,V               
  120   R   ARG152: 0.307   4* -0.570, 1.214     7,1     3/29 D,R               
  120   R       4* D,R               
  121   I   ILE153: 0.330   4* -0.570, 1.214     7,1     3/29 H,I               
  121   I       4* H,I               
  122   D   ASP154: -0.429   6* -1.107, 0.016     8,5     3/29 D,N               
  122   D       6* D,N               
  123   M   MET155: -0.296   6* -0.986, 0.016     8,5     3/29 L,M               
  123   M       6* L,M               
  124   V   VAL156: -0.946   8* -1.455,-0.721     9,7     3/29 V               
  124   V       8* V               
  125   V   VAL157: -0.137   5* -0.859, 0.294     8,4     3/29 L,V               
  125   V       5* L,V               
  126   R   ARG158: 0.277   4* -0.570, 1.214     7,1     3/29 R,Y               
  126   R       4* R,Y               
  127   L   LEU159: -0.174   6* -0.859, 0.294     8,4     3/29 L,V               
  127   L       6* L,V               
  128   R   ARG160: -0.959   8* -1.455,-0.721     9,7     3/29 R                 
  128   R       8* R                 
  129   K   LYS161: -0.914   8* -1.455,-0.721     9,7     3/29 K                 
  129   K       8* K                 
  130   K   LYS162: -0.914   8* -1.455,-0.721     9,7     3/29 K                 
  130   K       8* K                 
  131   R   ARG163: -0.419   6* -1.107, 0.016     8,5     3/29 K,R               
  131   R       6* K,R               






=Structure of the Proposed Irr Protein=
=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'/>
<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/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}}




Line 276: Line 277:


121 ylenshelvd iedphlalsk mpevpegyei aridmvvrlr kkr
121 ylenshelvd iedphlalsk mpevpegyei aridmvvrlr kkr




Line 288: Line 303:
=References=
=References=
<references/>
<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.
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.
4. You can edit your protein by using the scene authoring tools after loading the applet.
Retrieved from "https://proteopedia.openfox.io/w/User:Adam_Meade/Sandbox_1"