1jc5: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Crystal Structure of Native Methylmalonyl-CoA Epimerase==
==Crystal Structure of Native Methylmalonyl-CoA Epimerase==
<StructureSection load='1jc5' size='340' side='right' caption='[[1jc5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1jc5' size='340' side='right'caption='[[1jc5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1jc5]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"propionibacterium_shermanii"_van_niel_1928 "propionibacterium shermanii" van niel 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JC5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1jc5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JC5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jc4|1jc4]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylmalonyl-CoA_epimerase Methylmalonyl-CoA epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.1 5.1.99.1] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jc5 OCA], [https://pdbe.org/1jc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jc5 RCSB], [https://www.ebi.ac.uk/pdbsum/1jc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jc5 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jc5 OCA], [http://pdbe.org/1jc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jc5 RCSB], [http://www.ebi.ac.uk/pdbsum/1jc5 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8VQN0_PROFR Q8VQN0_PROFR]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jc5_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jc5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=1jc5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Methylmalonyl-CoA epimerase (MMCE) is an essential enzyme in the breakdown of odd-numbered fatty acids and of the amino acids valine, isoleucine, and methionine. Present in many bacteria and in animals, it catalyzes the conversion of (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, the substrate for the B12-dependent enzyme, methylmalonyl-CoA mutase. Defects in this pathway can result in severe acidosis and cause damage to the central nervous system in humans. RESULTS: The crystal structure of MMCE from Propionibacterium shermanii has been determined at 2.0 A resolution. The MMCE monomer is folded into two tandem betaalphabetabetabeta modules that pack edge-to-edge to generate an 8-stranded beta sheet. Two monomers then pack back-to-back to create a tightly associated dimer. In each monomer, the beta sheet curves around to create a deep cleft, in the floor of which His12, Gln65, His91, and Glu141 provide a binding site for a divalent metal ion, as shown by the binding of Co2+. Modeling 2-methylmalonate into the active site identifies two glutamate residues as the likely essential bases for the epimerization reaction. CONCLUSIONS: The betaalphabetabetabeta modules of MMCE correspond with those found in several other proteins, including bleomycin resistance protein, glyoxalase I, and a family of extradiol dioxygenases. Differences in connectivity are consistent with the evolution of these very different proteins from a common precursor by mechanisms of gene duplication and domain swapping. The metal binding residues also align precisely, and striking structural similarities between MMCE and glyoxalase I suggest common mechanisms in their respective epimerization and isomerization reactions.
Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold.,McCarthy AA, Baker HM, Shewry SC, Patchett ML, Baker EN Structure. 2001 Jul 3;9(7):637-46. PMID:11470438<ref>PMID:11470438</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jc5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Propionibacterium shermanii van niel 1928]]
[[Category: Large Structures]]
[[Category: Methylmalonyl-CoA epimerase]]
[[Category: Propionibacterium freudenreichii subsp. shermanii]]
[[Category: Baker, E N]]
[[Category: Baker EN]]
[[Category: Baker, H M]]
[[Category: Baker HM]]
[[Category: Carthy, A A.Mc]]
[[Category: Mc Carthy AA]]
[[Category: Patchett, M L]]
[[Category: Patchett ML]]
[[Category: Shewry, S C]]
[[Category: Shewry SC]]
[[Category: Epimerisation]]
[[Category: Isomerase]]
[[Category: Metal-assisted catalysis]]
[[Category: Methylmalonyl-coa]]
[[Category: Vicinal oxygen chelate superfamily]]

Latest revision as of 10:38, 7 February 2024

Crystal Structure of Native Methylmalonyl-CoA EpimeraseCrystal Structure of Native Methylmalonyl-CoA Epimerase

Structural highlights

1jc5 is a 6 chain structure with sequence from Propionibacterium freudenreichii subsp. shermanii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8VQN0_PROFR

Evolutionary Conservation

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

1jc5, resolution 2.20Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1jc5&oldid=4045217"