3cf4: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3cf4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_barkeri Methanosarcina barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CF4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3cf4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_barkeri Methanosarcina barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CF4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=WCC:FE(3)-NI(1)-S(4)+CLUSTER'>WCC</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&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.2 1.2.99.2] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=WCC:FE(3)-NI(1)-S(4)+CLUSTER'>WCC</scene></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=3cf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cf4 OCA], [https://pdbe.org/3cf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cf4 RCSB], [https://www.ebi.ac.uk/pdbsum/3cf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cf4 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=3cf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cf4 OCA], [https://pdbe.org/3cf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cf4 RCSB], [https://www.ebi.ac.uk/pdbsum/3cf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cf4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ACDA1_METBF ACDA1_METBF] Part of the ACDS complex that catalyzes the reversible cleavage of acetyl-CoA, allowing growth on acetate as sole source of carbon and energy. The alpha-epsilon subcomponent functions as a carbon monoxide dehydrogenase.[HAMAP-Rule:MF_01137]<ref>PMID:6425262</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=3cf4 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=3cf4 ConSurf].
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<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ni-dependent carbon monoxide dehydrogenases (Ni-CODHs) are a diverse family of enzymes that catalyze reversible CO:CO(2) oxidoreductase activity in acetogens, methanogens, and some CO-using bacteria. Crystallography of Ni-CODHs from CO-using bacteria and acetogens has revealed the overall fold of the Ni-CODH core and has suggested structures for the C cluster that mediates CO:CO(2) interconversion. Despite these advances, the mechanism of CO oxidation has remained elusive. Herein, we report the structure of a distinct class of Ni-CODH from methanogenic archaea: the alpha(2)epsilon(2) component from the alpha(8)beta(8)gamma(8)delta(8)epsilon(8) CODH/acetyl-CoA decarbonylase/synthase complex, an enzyme responsible for the majority of biogenic methane production on Earth. The structure of this Ni-CODH component provides support for a hitherto unobserved state in which both CO and H(2)O/OH(-) bind to the Ni and the exogenous FCII iron of the C cluster, respectively, and offers insight into the structures and functional roles of the epsilon-subunit and FeS domain not present in nonmethanogenic Ni-CODHs.
Structure of the alpha2epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex.,Gong W, Hao B, Wei Z, Ferguson DJ Jr, Tallant T, Krzycki JA, Chan MK Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9558-63. Epub 2008 Jul 9. PMID:18621675<ref>PMID:18621675</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3cf4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Methanosarcina barkeri]]
[[Category: Methanosarcina barkeri]]
[[Category: Chan, M K]]
[[Category: Chan MK]]
[[Category: Ferguson, D J]]
[[Category: Ferguson Jr DJ]]
[[Category: Gong, W]]
[[Category: Gong W]]
[[Category: Hao, B]]
[[Category: Hao B]]
[[Category: Krzycki, J A]]
[[Category: Krzycki JA]]
[[Category: Tallant, T]]
[[Category: Tallant T]]
[[Category: Wei, Z]]
[[Category: Wei Z]]
[[Category: 4fe-ni-4]]
[[Category: Iron-nikel-sulfur]]
[[Category: Methanomicrobia]]
[[Category: Oxidoreductase]]

Latest revision as of 12:35, 21 February 2024

Structure of the CODH component of the M. barkeri ACDS complexStructure of the CODH component of the M. barkeri ACDS complex

Structural highlights

3cf4 is a 2 chain structure with sequence from Methanosarcina barkeri. 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

ACDA1_METBF Part of the ACDS complex that catalyzes the reversible cleavage of acetyl-CoA, allowing growth on acetate as sole source of carbon and energy. The alpha-epsilon subcomponent functions as a carbon monoxide dehydrogenase.[HAMAP-Rule:MF_01137][1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Krzycki JA, Zeikus JG. Characterization and purification of carbon monoxide dehydrogenase from Methanosarcina barkeri. J Bacteriol. 1984 Apr;158(1):231-7. PMID:6425262 doi:10.1128/jb.158.1.231-237.1984

3cf4, resolution 2.00Å

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