5HLU | pdb_00005hlu

X-ray crystal structure of met F43H/H64A sperm whale myoglobin in complex with nitric oxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.159 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center

Wu, L.B.Yuan, H.Gao, S.Q.You, Y.Nie, C.M.Wen, G.B.Lin, Y.W.Tan, X.

(2016) Nitric Oxide 57: 21-29

  • DOI: https://doi.org/10.1016/j.niox.2016.04.007
  • Primary Citation Related Structures: 
    5HLQ, 5HLU, 5HLX

  • PubMed Abstract: 

    Heme proteins perform diverse functions in living systems, of which nitrite reductase (NIR) activity receives much attention recently. In this study, to better understand the structural elements responsible for the NIR activity, we used myoglobin (Mb) as a model heme protein and redesigned the heme active center, by introducing one or two distal histidines, and by creating a channel to the heme center with removal of the native distal His64 gate (His to Ala mutation). UV-Vis kinetic studies, combined with EPR studies, showed that a single distal histidine with a suitable position to the heme iron, i.e., His43, is crucial for nitrite (NO2(-)) to nitric oxide (NO) reduction. Moreover, creation of a water channel to the heme center significantly enhanced the NIR activity compared to the corresponding mutant without the channel. In addition, X-ray crystallographic studies of F43H/H64A Mb and its complexes with NO2(-) or NO revealed a unique hydrogen-bonding network in the heme active center, as well as unique substrate and product binding models, providing valuable structural information for the enhanced NIR activity. These findings enriched our understanding of the structure and NIR activity relationship of heme proteins. The approach of creating a channel in this study is also useful for rational design of other functional heme proteins.


  • Organizational Affiliation
    • School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.

Macromolecule Content 

  • Total Structure Weight: 17.81 kDa 
  • Atom Count: 1,539 
  • Modeled Residue Count: 152 
  • Deposited Residue Count: 153 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myoglobin153Physeter macrocephalusMutation(s): 2 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.159 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.69α = 90
b = 49.528β = 90
c = 77.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-05-25 
  • Deposition Author(s): Yuan, H.

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description