4XPY

Crystal structure of hemerythrin : L114Y mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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This is version 1.4 of the entry. See complete history


Literature

The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel.

Chen, K.H.C.Chuankhayan, P.Wu, H.H.Chen, C.J.Fukuda, M.Yu, S.S.F.Chan, S.I.

(2015) J Inorg Biochem 150: 81-89

  • DOI: https://doi.org/10.1016/j.jinorgbio.2015.04.001
  • Primary Citation of Related Structures:  
    4XPW, 4XPX, 4XPY, 4XQ1

  • PubMed Abstract: 

    The bacteriohemerythrin (McHr) from Methylococcus capsulatus (Bath) is an oxygen carrier that serves as a transporter to deliver O2 from the cytosol of the bacterial cell body to the particulate methane monooxygenase residing in the intracytoplasmic membranes for methane oxidation. Here we report X-ray protein crystal structures of the recombinant wild type (WT) McHr and its L114A, L114Y and L114F mutants. The structure of the WT reveals a possible water tunnel in the McHr that might be linked to its faster autoxidation relative to hemerythrin in marine invertebrates. With Leu114 positioned at the end of this putative water tunnel, the hydrophobic side chain of this residue seems to play a prominent role in controlling the access of the water molecule required for autoxidation. This hypothesis is examined by comparing the autoxidation rates of the WT McHr with those of the L114A, L114Y and L114F mutants. The biochemical data are correlated with structural insights derived from the analysis of the putative water tunnels in the various McHr proteins provided by the X-ray structures.


  • Organizational Affiliation

    Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 30076 Hsinchu, Taiwan; Department of Biotechnology and Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan; Department of Physics, National Tsing Hua University, Hsinchu 30014, Taiwan. Electronic address: cjchen@nsrrc.org.tw.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriohemerythrin131Methylococcus capsulatus str. BathMutation(s): 0 
UniProt
Find proteins for Q60AX2 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q60AX2 
Go to UniProtKB:  Q60AX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60AX2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.112α = 90
b = 83.112β = 90
c = 31.013γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2015-12-09
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description