2WSM | pdb_00002wsm

Crystal structure of Hydrogenase Maturation Factor HypB From Archaeoglobus Fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.275 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structural Basis for GTP-Dependent Dimerization of Hydrogenase Maturation Factor Hypb.

Chan, K.H.Li, T.Wong, C.Wong, K.B.

(2012) PLoS One 7: 30547

  • DOI: https://doi.org/10.1371/journal.pone.0030547
  • Primary Citation Related Structures: 
    2WSM

  • PubMed Abstract: 

    Maturation of [NiFe]-hydrogenase requires the insertion of iron, cyanide and carbon monoxide, followed by nickel, to the catalytic core of the enzyme. Hydrogenase maturation factor HypB is a metal-binding GTPase that is essential for the nickel delivery to the hydrogenase. Here we report the crystal structure of Archeoglobus fulgidus HypB (AfHypB) in apo-form. We showed that AfHypB recognizes guanine nucleotide using Asp-194 on the G5 loop despite having a non-canonical NKxA G4-motif. Structural comparison with the GTPγS-bound Methanocaldococcus jannaschii HypB identifies conformational changes in the switch I region, which bring an invariant Asp-72 to form an intermolecular salt-bridge with another invariant residue Lys-148 upon GTP binding. Substitution of K148A abolished GTP-dependent dimerization of AfHypB, but had no significant effect on the guanine nucleotide binding and on the intrinsic GTPase activity. In vivo complementation study in Escherichia coli showed that the invariant lysine residue is required for in vivo maturation of hydrogenase. Taken together, our results suggest that GTP-dependent dimerization of HypB is essential for hydrogenase maturation. It is likely that a nickel ion is loaded to an extra metal binding site at the dimeric interface of GTP-bound HypB and transferred to the hydrogenase upon GTP hydrolysis.


  • Organizational Affiliation
    • Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, The People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 49.43 kDa 
  • Atom Count: 3,157 
  • Modeled Residue Count: 390 
  • Deposited Residue Count: 442 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPB)
A, B
221Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
UniProt
Find proteins for O28903 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28903 
Go to UniProtKB:  O28903
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28903
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.275 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.494α = 90
b = 82.325β = 90
c = 68.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary