2OYY

HTHP: a hexameric tyrosine-coordinated heme protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

HTHP: A Novel Class of Hexameric, Tyrosine-coordinated Heme Proteins

Jeoung, J.H.Pippig, D.A.Martins, B.M.Wagener, N.Dobbek, H.

(2007) J Mol Biol 368: 1122-1131

  • DOI: https://doi.org/10.1016/j.jmb.2007.02.079
  • Primary Citation of Related Structures:  
    2OYY

  • PubMed Abstract: 

    We have cloned, expressed, isolated and characterized a hexameric tyrosine-coordinated heme protein (HTHP) from the marine bacterium Silicibacter pomeroyi. HTHP shows peroxidase and catalase activity and has a high thermal stability. As-isolated HTHP has absorption maxima at 407, 495, 504, 532 and 622 nm wavelength. Upon reduction maxima at 430, 564 and 596 nm wavelength are discernible. The crystal structure of HTHP reveals a hexameric, ring-like arrangement of six monomers. Each monomer binds a solvent accessible heme group, which is stabilized by the interaction of three neighboring monomers. The pocket around the heme distal side is positively charged due to three conserved arginine residues in direct vicinity. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand. The coordinating hydroxyl-group of the tyrosine ligand interacts with the guanidinium group of a nearby arginine residue, an arrangement closely resembling the catalytic dyad found in monofunctional heme-containing catalases and coral allene oxide synthases, which are b-type cytochromes with tyrosine coordination trans to an empty coordination site. Despite the similarity in heme coordination HTHP is functionally and structurally unrelated to catalases and other heme-containing proteins. Its hexameric arrangement, solvent accessible heme binding pocket and heme coordination by tyrosine render HTHP a unique protein with unusual properties. A database search against complete and incomplete genomes shows that the 76 amino acid residues sequence of HTHP is unrelated to characterized proteins, but is homologous to orfs found in a phylogenetically diverse set of bacteria with sequence identities of 30-76%. We therefore propose that HTHP is the prototype of a new class of heme proteins.


  • Organizational Affiliation

    Laboratorium Proteinkristallographie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hexameric cytochrome
A, B, C, D, E
A, B, C, D, E, F, G, H
76Ruegeria pomeroyiMutation(s): 0 
Gene Names: spoa0176
UniProt
Find proteins for Q5LL55 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore Q5LL55 
Go to UniProtKB:  Q5LL55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LL55
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth H]
J [auth A]
M [auth B]
P [auth C]
S [auth D]
BA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
X [auth F],
Z [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
K [auth B]
L [auth B]
N [auth C]
AA [auth H],
I [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
W [auth F],
Y [auth G]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.71α = 90
b = 173.71β = 90
c = 45.88γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHARPphasing
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2007-04-10 
  • Deposition Author(s): Dobbek, H.

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description