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PDBsum entry 2z8y
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase/transferase PDB id
2z8y

 

 

 

 

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Contents
Protein chains
673 a.a. *
728 a.a. *
Ligands
SF4 ×10
XCC ×4
_XE ×38
GOL ×11
Metals
CU1 ×4
_NI ×4
Waters ×1153
* Residue conservation analysis
PDB id:
2z8y
Name: Oxidoreductase/transferase
Title: Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs) from moorella thermoacetica
Structure: Carbon monoxide dehydrogenase/acetyl coa synthase subunit beta. Chain: a, b, c, d. Synonym: carbon monoxide dehydrogenase subunit, codh/acs, codh subunit. Carbon monoxide dehydrogenase/acetyl coa synthase subunit alpha. Chain: m, n, o, p. Synonym: acetyl coa synthase subunit, codh/acs, acs subunit.
Source: Moorella thermoacetica. Organism_taxid: 1525. Organism_taxid: 1525
Resolution:
2.51Å     R-factor:   0.182     R-free:   0.250
Authors: T.I.Doukov,L.C.Blasiak,C.L.Drennan
Key ref: T.I.Doukov et al. (2008). Xenon in and at the end of the tunnel of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Biochemistry, 47, 3474-3483. PubMed id: 18293927
Date:
12-Sep-07     Release date:   11-Mar-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P27989  (DCMB_MOOTH) -  Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta from Moorella thermoacetica
Seq:
Struc: 		 
Seq:
Struc: 		674 a.a.
673 a.a.
Protein chains
Pfam   ArchSchema ?
P27988  (DCMA_MOOTH) -  Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha from Moorella thermoacetica
Seq:
Struc: 		 
Seq:
Struc: 		729 a.a.
728 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, B, C, D: E.C.1.2.7.4  - anaerobic carbon-monoxide dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: CO + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O = 2 reduced [2Fe-2S]- [ferredoxin] + CO2 + 2 H+
CO
 + 2 × oxidized [2Fe-2S]-[ferredoxin]
 + H2O
 = 2 × reduced [2Fe-2S]- [ferredoxin]
 + CO2
 + 2 × H(+)
      Cofactor: Fe cation; Ni(2+); Zn(2+)
   Enzyme class 3: Chains M, N, O, P: E.C.2.3.1.169  - CO-methylating acetyl-CoA synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Co(I)-[corrinoid Fe-S protein] + acetyl-CoA + H+ = methyl-Co(III)- [corrinoid Fe-S protein] + CO + CoA
Co(I)-[corrinoid Fe-S protein]
 + 2 × acetyl-CoA
 + H(+)
 = 2 × methyl-Co(III)- [corrinoid Fe-S protein]
 + CO
 + 2 × CoA
      Cofactor: Cu(2+); Iron-sulfur; Ni(2+)
Cu(2+)
 Iron-sulfur
 Ni(2+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Biochemistry 47:3474-3483 (2008)
PubMed id: 18293927  
 
 
Xenon in and at the end of the tunnel of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
T.I.Doukov, L.C.Blasiak, J.Seravalli, S.W.Ragsdale, C.L.Drennan.
 
  ABSTRACT  
 
A fascinating feature of some bifunctional enzymes is the presence of an internal channel or tunnel to connect the multiple active sites. A channel can allow for a reaction intermediate generated at one active site to be used as a substrate at a second active site, without the need for the intermediate to leave the safety of the protein matrix. One such bifunctional enzyme is carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica (mtCODH/ACS). A key player in the global carbon cycle, CODH/ACS uses a Ni-Fe-S center called the C-cluster to reduce carbon dioxide to carbon monoxide and uses a second Ni-Fe-S center, called the A-cluster, to assemble acetyl-CoA from a methyl group, coenzyme A, and C-cluster-generated CO. mtCODH/ACS has been proposed to contain one of the longest enzyme channels (138 A long) to allow for intermolecular CO transport. Here, we report a 2.5 A resolution structure of xenon-pressurized mtCODH/ACS and examine the nature of gaseous cavities within this enzyme. We find that the cavity calculation program CAVENV accurately predicts the channels connecting the C- and A-clusters, with 17 of 19 xenon binding sites within the predicted regions. Using this X-ray data, we analyze the amino acid composition surrounding the 19 Xe sites and consider how the protein fold is utilized to carve out such an impressive interior passageway. Finally, structural comparisons of Xe-pressurized mtCODH/ACS with related enzyme structures allow us to study channel design principles, as well as consider the conformational flexibility of an enzyme that contains a cavity through its center.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21130022 Y.Kung, and C.L.Drennan (2011).
A role for nickel-iron cofactors in biological carbon monoxide and carbon dioxide utilization.
  Curr Opin Chem Biol, 15, 276-283.  
  19241380 A.S.Olia, S.Casjens, and G.Cingolani (2009).
Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.
  Protein Sci, 18, 537-548.
PDB code: 3c9i
19650626 A.Volbeda, C.Darnault, X.Tan, P.A.Lindahl, and J.C.Fontecilla-Camps (2009).
Novel domain arrangement in the crystal structure of a truncated acetyl-CoA synthase from Moorella thermoacetica.
  Biochemistry, 48, 7916-7926.
PDB code: 3git
19458968 B.M.Barney, M.G.Yurth, P.C.Dos Santos, D.R.Dean, and L.C.Seefeldt (2009).
A substrate channel in the nitrogenase MoFe protein.
  J Biol Inorg Chem, 14, 1015-1022.  
19675641 J.C.Fontecilla-Camps, P.Amara, C.Cavazza, Y.Nicolet, and A.Volbeda (2009).
Structure-function relationships of anaerobic gas-processing metalloenzymes.
  Nature, 460, 814-822.  
18851709 M.D.Fayer (2009).
Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy.
  Annu Rev Phys Chem, 60, 21-38.  
19363030 S.W.Ragsdale (2009).
Nickel-based Enzyme Systems.
  J Biol Chem, 284, 18571-18575.  
19583207 Y.Kung, T.I.Doukov, J.Seravalli, S.W.Ragsdale, and C.L.Drennan (2009).
Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
  Biochemistry, 48, 7432-7440.
PDB codes: 3i01 3i04
18562286 H.Ishikawa, K.Kwak, J.K.Chung, S.Kim, and M.D.Fayer (2008).
Direct observation of fast protein conformational switching.
  Proc Natl Acad Sci U S A, 105, 8619-8624.  
18839332 J.W.Murray, K.Maghlaoui, J.Kargul, M.Sugiura, and J.Barber (2008).
Analysis of xenon binding to photosystem II by X-ray crystallography.
  Photosynth Res, 98, 523-527.  
18801467 S.W.Ragsdale, and E.Pierce (2008).
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation.
  Biochim Biophys Acta, 1784, 1873-1898.  
18804699 S.W.Ragsdale (2008).
Catalysis of methyl group transfers involving tetrahydrofolate and B(12).
  Vitam Horm, 79, 293-324.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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