1kgp: Difference between revisions

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[[Image:1kgp.jpg|left|200px]]


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==R2F from Corynebacterium Ammoniagenes in its Mn substituted form==
The line below this paragraph, containing "STRUCTURE_1kgp", creates the "Structure Box" on the page.
<StructureSection load='1kgp' size='340' side='right'caption='[[1kgp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1kgp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_ammoniagenes Corynebacterium ammoniagenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KGP FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
{{STRUCTURE_1kgp| PDB=1kgp |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kgp OCA], [https://pdbe.org/1kgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kgp RCSB], [https://www.ebi.ac.uk/pdbsum/1kgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kgp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O69274_CORAM O69274_CORAM] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/1kgp_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kgp ConSurf].
<div style="clear:both"></div>


'''R2F from Corynebacterium Ammoniagenes in its Mn substituted form'''
==See Also==
 
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Ribonucleotide reductase (RNR) is the enzyme performing de novo production of the four deoxyribonucleotides needed for DNA synthesis. All mammals as well as some prokaryotes express the class I enzyme which is an alpha(2)beta(2) protein. The smaller of the homodimers, denoted R2, contains a di-iron carboxylate site which, upon reaction with molecular oxygen, generates a stable tyrosyl radical needed for catalysis. The three-dimensional structure of the oxidized class Ib RNR R2 from Corynebacterium ammoniagenes has been determined at 1.85 A resolution and refined to an R-value of 15.8% (R(free) = 21.3%). In addition, structures of both the reduced iron-containing, and manganese-substituted protein have been solved. The C. ammoniagenes R2 has been proposed to be manganese-dependent. The present structure provides evidence that manganese is not oxidized by the protein, in agreement with recent biochemical data, and that no obvious structural abnormalities are seen in the oxidized and reduced iron-containing forms, giving further support that the protein is indeed an iron-dependent RNR R2. The di-manganese structure also provides an explanation for the magnetic properties of this site. The structure of the oxidized C. ammoniagenes R2 also reveals an additional water molecule bridging the radical and the iron site, which has not previously been seen in any other R2 structure and which might have important mechanistic implications.
 
==About this Structure==
1KGP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_ammoniagenes Corynebacterium ammoniagenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGP OCA].
 
==Reference==
Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes., Hogbom M, Huque Y, Sjoberg BM, Nordlund P, Biochemistry. 2002 Jan 29;41(4):1381-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11802741 11802741]
[[Category: Corynebacterium ammoniagenes]]
[[Category: Corynebacterium ammoniagenes]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hogbom, M.]]
[[Category: Hogbom M]]
[[Category: Huque, Y.]]
[[Category: Huque Y]]
[[Category: Nordlund, P.]]
[[Category: Nordlund P]]
[[Category: Sjoberg, B M.]]
[[Category: Sjoberg BM]]
[[Category: Arm exchange]]
[[Category: Helix bundle]]
[[Category: Radical protein]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:43:33 2008''

Latest revision as of 16:25, 13 March 2024

R2F from Corynebacterium Ammoniagenes in its Mn substituted formR2F from Corynebacterium Ammoniagenes in its Mn substituted form

Structural highlights

1kgp is a 4 chain structure with sequence from Corynebacterium ammoniagenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O69274_CORAM Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1kgp, resolution 2.00Å

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