6U9J | pdb_00006u9j

Crystal structure of ChuX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.234 (DCC) 
  • R-Value Work: 
    0.209 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6U9J

This is version 1.2 of the entry. See complete history

Literature

New Insight into the Mechanism of Anaerobic Heme Degradation.

Mathew, L.G.Beattie, N.R.Pritchett, C.Lanzilotta, W.N.

(2019) Biochemistry 58: 4641-4654

  • DOI: https://doi.org/10.1021/acs.biochem.9b00841
  • Primary Citation Related Structures: 
    6U9J

  • PubMed Abstract: 

    ChuW, ChuX, and ChuY are contiguous genes downstream from a single promoter that are expressed in the enteric pathogen Escherichia coli O157:H7 when iron is limiting. These genes, and the corresponding proteins, are part of a larger heme uptake and utilization operon that is common to several other enteric pathogens, such as Vibrio cholerae . The aerobic degradation of heme has been well characterized in humans and several pathogenic bacteria, including E. coli O157:H7, but only recently was it shown that ChuW catalyzes the anaerobic degradation of heme to release iron and produce a reactive tetrapyrrole termed "anaerobilin". ChuY has been shown to function as an anaerobilin reductase, in a role that parallels biliverdin reductase. In this work we have employed biochemical and biophysical approaches to further interrogate the mechanism of the anaerobic degradation of heme. We demonstrate that the iron atom of the heme does not participate in the catalytic mechanism of ChuW and that S- adenosyl-l-methionine binding induces conformational changes that favor catalysis. In addition, we show that ChuX and ChuY have synergistic and additive effects on the turnover rate of ChuW. Finally, we have found that ChuS is an effective source of heme or protoporphyrin IX for ChuW under anaerobic conditions. These data indicate that ChuS may have dual functionality in vivo. Specifically, ChuS serves as a heme oxygenase during aerobic metabolism of heme but functions as a cytoplasmic heme storage protein under anaerobic conditions, akin to what has been shown for PhuS (45% sequence identity) from Pseudomonas aeruginosa.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies , University of Georgia , Athens , Georgia 30602 , United States.

Macromolecule Content 

  • Total Structure Weight: 71.89 kDa 
  • Atom Count: 5,553 
  • Modeled Residue Count: 637 
  • Deposited Residue Count: 640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heme utilization carrier protein
A, B, C, D
160Escherichia coli O157:H7Mutation(s): 0 
Gene Names: hutXCAM50_0001390ECs_4384FGA21_01415FGA23_01320
UniProt
Find proteins for Q8X5N5 (Escherichia coli O157:H7)
Explore Q8X5N5 
Go to UniProtKB:  Q8X5N5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X5N5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.234 (DCC) 
  • R-Value Work:  0.209 (DCC) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.566α = 90
b = 50.566β = 90
c = 208.969γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124203

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Advisory, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description