6VNA | pdb_00006vna

Pden_1323


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.259 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.221 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 6VNA

This is version 1.2 of the entry. See complete history

Literature

A noncanonical heme oxygenase specific for the degradation of c-type heme.

Li, S.Isiorho, E.A.Owens, V.L.Donnan, P.H.Odili, C.L.Mansoorabadi, S.O.

(2021) J Biological Chem 296: 100666-100666

  • DOI: https://doi.org/10.1016/j.jbc.2021.100666
  • Primary Citation Related Structures: 
    6VNA

  • PubMed Abstract: 

    Heme oxygenases (HOs) play a critical role in recouping iron from the labile heme pool. The acquisition and liberation of heme iron are especially important for the survival of pathogenic bacteria. All characterized HOs, including those belonging to the HugZ superfamily, preferentially cleave free b-type heme. Another common form of heme found in nature is c-type heme, which is covalently linked to proteinaceous cysteine residues. However, mechanisms for direct iron acquisition from the c-type heme pool are unknown. Here we identify a HugZ homolog from the oligopeptide permease (opp) gene cluster of Paracoccus denitrificans that lacks any observable reactivity with heme b and show that it instead rapidly degrades c-type hemopeptides. This c-type heme oxygenase catalyzes the oxidative cleavage of the model substrate microperoxidase-11 at the β- and/or δ-meso position(s), yielding the corresponding peptide-linked biliverdin, CO, and free iron. X-ray crystallographic analysis suggests that the switch in substrate specificity from b-to c-type heme involves loss of the N-terminal α/β domain and C-terminal loop containing the coordinating histidine residue characteristic of HugZ homologs, thereby accommodating a larger substrate that provides its own iron ligand. These structural features are also absent in certain heme utilization/storage proteins from human pathogens that exhibit low or no HO activity with free heme. This study thus expands the scope of known iron acquisition strategies to include direct oxidative cleavage of heme-containing proteolytic fragments of c-type cytochromes and helps to explain why certain oligopeptide permeases show specificity for the import of heme in addition to peptides.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA.

Macromolecule Content 

  • Total Structure Weight: 52.11 kDa 
  • Atom Count: 3,204 
  • Modeled Residue Count: 419 
  • Deposited Residue Count: 483 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
A, B, C
161Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: Pden_1323Pden_1574
UniProt
Find proteins for A1B1N4 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B1N4 
Go to UniProtKB:  A1B1N4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B1N4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.221 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.843α = 90
b = 117.044β = 99.376
c = 59.382γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description