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PDBsum entry 2e7z
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protein ligands metals links
Lyase PDB id
2e7z

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
727 a.a. *
Ligands
ACT
SF4
MGD ×2
MPD ×2
Metals
_NA
__W
Waters ×912
* Residue conservation analysis
PDB id:
2e7z
Name: Lyase
Title: Acetylene hydratase from pelobacter acetylenicus
Structure: Acetylene hydratase ahy. Chain: a. Ec: 4.2.1.71
Source: Pelobacter acetylenicus. Organism_taxid: 29542. Strain: woacy
Resolution:
1.26Å     R-factor:   0.161     R-free:   0.195
Authors: O.Einsle,P.M.H.Kroneck,G.B.Seiffert,A.Messerschmidt
Key ref:
G.B.Seiffert et al. (2007). Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase. Proc Natl Acad Sci U S A, 104, 3073-3077. PubMed id: 17360611 DOI: 10.1073/pnas.0610407104
Date:
15-Jan-07     Release date:   27-Feb-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q71EW5  (AHY_SYNAC) -  Acetylene hydratase from Syntrophotalea acetylenica
Seq:
Struc: 		 
Seq:
Struc: 		730 a.a.
727 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.112  - acetylene hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: acetaldehyde = acetylene + H2O
acetaldehyde
Bound ligand (Het Group name = ACT)
matches with 75.00% similarity 		= acetylene
 + H2O
      Cofactor: Iron-sulfur; Mo-bis(molybdopterin guanine dinucleotide); W cation
Iron-sulfur
 Mo-bis(molybdopterin guanine dinucleotide)
 W cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0610407104 Proc Natl Acad Sci U S A 104:3073-3077 (2007)
PubMed id: 17360611  
 
 
Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase.
G.B.Seiffert, G.M.Ullmann, A.Messerschmidt, B.Schink, P.M.Kroneck, O.Einsle.
 
  ABSTRACT  
 
The tungsten-iron-sulfur enzyme acetylene hydratase stands out from its class because it catalyzes a nonredox reaction, the hydration of acetylene to acetaldehyde. Sequence comparisons group the protein into the dimethyl sulfoxide reductase family, and it contains a bis-molybdopterin guanine dinucleotide-ligated tungsten atom and a cubane-type [4Fe:4S] cluster. The crystal structure of acetylene hydratase at 1.26 A now shows that the tungsten center binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct, hydrophobic pocket. This mechanism requires a strong shift of pK(a) of the aspartate, caused by a nearby low-potential [4Fe:4S] cluster. To access this previously unrecognized W-Asp active site, the protein evolved a new substrate channel distant from where it is found in other molybdenum and tungsten enzymes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of acetylene hydratase from P. acetylenicus. The stereo representation shows an orientation viewing down the active site channel as seen in Fig. 4A. 		Figure 3.
Fig. 3. Cofactors and active site of AH. (A) The tungsten atom (blue) is coordinated by the dithiolene groups of both MGD cofactors and the side chain of Cys-141. A water molecule completes the slightly distorted octahedral geometry. This water is also hydrogen-bonded to Asp-13, a residue adjacent to the [4Fe:4S] cluster ligand Cys-12. (B) Above the bound water molecule, a ring of hydrophobic residues forms the bottom of the active site access channel (see Fig. 4).
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21120472 J.Jin, A.J.Straathof, M.W.Pinkse, and U.Hanefeld (2011).
Purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity.
  Appl Microbiol Biotechnol, 89, 1831-1840.  
21243161 J.Jin, and U.Hanefeld (2011).
The selective addition of water to C=C bonds; enzymes are the best chemists.
  Chem Commun (Camb), 47, 2502-2510.  
21186382 P.V.Bernhardt (2011).
Exploiting the versatility and selectivity of Mo enzymes with electrochemistry.
  Chem Commun (Camb), 47, 1663-1673.  
20495719 A.Döring, and C.Schulzke (2010).
Tungsten's redox potential is more temperature sensitive than that of molybdenum.
  Dalton Trans, 39, 5623-5629.  
20369217 M.A.Vincent, I.H.Hillier, G.Periyasamy, and N.A.Burton (2010).
A DFT study of the possible role of vinylidene and carbene intermediates in the mechanism of the enzyme acetylene hydratase.
  Dalton Trans, 39, 3816-3822.  
19626353 M.S.Till, and G.M.Ullmann (2010).
McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm.
  J Mol Model, 16, 419-429.  
21149684 R.Z.Liao, J.G.Yu, and F.Himo (2010).
Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations.
  Proc Natl Acad Sci U S A, 107, 22523-22527.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
19206188 S.Groysman, and R.H.Holm (2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.
  Biochemistry, 48, 2310-2320.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
19020675 H.Sugimoto, and H.Tsukube (2008).
Chemical analogues relevant to molybdenum and tungsten enzyme reaction centres toward structural dynamics and reaction diversity.
  Chem Soc Rev, 37, 2609-2619.  
18096847 J.R.Andreesen, and K.Makdessi (2008).
Tungsten, the surprisingly positively acting heavy metal element for prokaryotes.
  Ann N Y Acad Sci, 1125, 215-229.  
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.

 

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