2E7Z | pdb_00002e7z

Acetylene Hydratase from Pelobacter acetylenicus

PDB DOI: https://doi.org/10.2210/pdb2E7Z/pdb

Classification: LYASE
Organism(s): Syntrophotalea acetylenica
Mutation(s): No

Deposited: 2007-01-15 Released: 2007-02-27
Deposition Author(s): Einsle, O., Kroneck, P.M.H., Seiffert, G.B., Messerschmidt, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free:
0.195 (Depositor), 0.192 (DCC)
R-Value Work:
0.160 (Depositor), 0.158 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase

Seiffert, G.B., Ullmann, G.M., Messerschmidt, A., Schink, B., Kroneck, P.M.H., Einsle, O.

(2007) Proc Natl Acad Sci U S A 104: 3073-3077

PubMed: 17360611 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0610407104
Primary Citation Related Structures:
2E7Z

PubMed 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.

Organizational Affiliation

Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany.

Macromolecule Content

Total Structure Weight: 83.99 kDa
Atom Count: 8,716
Modeled Residue Count: 727
Deposited Residue Count: 727
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylene hydratase Ahy	A	727	Syntrophotalea acetylenica	Mutation(s): 0 EC: 4.2.1.71 (PDB Primary Data), 4.2.1.112 (UniProt)
UniProt
Find proteins for Q71EW5 (Syntrophotalea acetylenica) Explore Q71EW5 Go to UniProtKB: Q71EW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71EW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
W Query on W Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.195 (Depositor), 0.192 (DCC)
R-Value Work: 0.160 (Depositor), 0.158 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.776	α = 90
b = 71.971	β = 124.26
c = 106.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 2.0: 2019-09-04
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-12-25
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary