1ef8: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ef8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EF8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ef8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EF8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.85&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ef9|1ef9]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methylmalonyl-CoA_decarboxylase Methylmalonyl-CoA decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.41 4.1.1.41] </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=1ef8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ef8 OCA], [https://pdbe.org/1ef8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ef8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ef8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ef8 ProSAT]</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=1ef8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ef8 OCA], [https://pdbe.org/1ef8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ef8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ef8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ef8 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SCPB_ECOLI SCPB_ECOLI]] Catalyzes the decarboxylation of methylmalonyl-CoA to propionyl-CoA. Could be part of a pathway that converts succinate to propionate.<ref>PMID:10769117</ref>
[https://www.uniprot.org/uniprot/SCPB_ECOLI SCPB_ECOLI] Catalyzes the decarboxylation of methylmalonyl-CoA to propionyl-CoA. Could be part of a pathway that converts succinate to propionate.<ref>PMID:10769117</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1ef8 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=1ef8 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The molecular structure of methylmalonyl CoA decarboxylase (MMCD), a newly defined member of the crotonase superfamily encoded by the Escherichia coli genome, has been solved by X-ray crystallographic analyses to a resolution of 1.85 A for the unliganded form and to a resolution of 2.7 A for a complex with an inert thioether analogue of methylmalonyl CoA. Like two other structurally characterized members of the crotonase superfamily (crotonase and dienoyl CoA isomerase), MMCD is a hexamer (dimer of trimers) with each polypeptide chain composed of two structural motifs. The larger N-terminal domain contains the active site while the smaller C-terminal motif is alpha-helical and involved primarily in trimerization. Unlike the other members of the crotonase superfamily, however, the C-terminal motif is folded back onto the N-terminal domain such that each active site is wholly contained within a single subunit. The carboxylate group of the thioether analogue of methylmalonyl CoA is hydrogen bonded to the peptidic NH group of Gly 110 and the imidazole ring of His 66. From modeling studies, it appears that Tyr 140 is positioned within the active site to participate in the decarboxylation reaction by orienting the carboxylate group of methylmalonyl CoA so that it is orthogonal to the plane of the thioester carbonyl group. Surprisingly, while the active site of MMCD contains Glu 113, which is homologous to the general acid/base Glu 144 in the active site of crotonase, its carboxylate side chain is hydrogen bonded to Arg 86, suggesting that it is not directly involved in catalysis. The new constellation of putative functional groups observed in the active site of MMCD underscores the diversity of function in this superfamily.
New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.,Benning MM, Haller T, Gerlt JA, Holden HM Biochemistry. 2000 Apr 25;39(16):4630-9. PMID:10769118<ref>PMID:10769118</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ef8" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Methylmalonyl-CoA decarboxylase]]
[[Category: Benning MM]]
[[Category: Benning, M M]]
[[Category: Gerlt JA]]
[[Category: Gerlt, J A]]
[[Category: Haller T]]
[[Category: Haller, T]]
[[Category: Holden HM]]
[[Category: Holden, H M]]
[[Category: Decarboxylase]]
[[Category: Lyase]]
[[Category: Methylmalonyl coa]]

Latest revision as of 10:01, 7 February 2024

CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASECRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE

Structural highlights

1ef8 is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCPB_ECOLI Catalyzes the decarboxylation of methylmalonyl-CoA to propionyl-CoA. Could be part of a pathway that converts succinate to propionate.[1]

Evolutionary Conservation

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

References

  1. ↑ Haller T, Buckel T, Retey J, Gerlt JA. Discovering new enzymes and metabolic pathways: conversion of succinate to propionate by Escherichia coli. Biochemistry. 2000 Apr 25;39(16):4622-9. PMID:10769117

1ef8, resolution 1.85Å

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