1BVB

HEME-PACKING MOTIFS REVEALED BY THE CRYSTAL STRUCTURE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Heme packing motifs revealed by the crystal structure of the tetra-heme cytochrome c554 from Nitrosomonas europaea.

Iverson, T.M.Arciero, D.M.Hsu, B.T.Logan, M.S.Hooper, A.B.Rees, D.C.

(1998) Nat.Struct.Mol.Biol. 5: 1005-1012

  • DOI: 10.1038/2975

  • PubMed Abstract: 
  • Cytochrome c554 (cyt c554), a tetra-heme cytochrome from Nitrosomonas europaea, is an essential component in the biological nitrification pathway. In N. europaea, ammonia is converted to hydroxylamine, which is then oxidized to nitrite by hydroxylami ...

    Cytochrome c554 (cyt c554), a tetra-heme cytochrome from Nitrosomonas europaea, is an essential component in the biological nitrification pathway. In N. europaea, ammonia is converted to hydroxylamine, which is then oxidized to nitrite by hydroxylamine oxidoreductase (HAO). Cyt c554 functions in the latter process by accepting pairs of electrons from HAO and transferring them to a cytochrome acceptor. The crystal structure of cyt c554 at 2.6 A resolution shows a predominantly alpha-helical protein with four covalently attached hemes. The four hemes are arranged in two pairs such that the planes of the porphyrin rings are almost parallel and overlapping at the edge; corresponding heme arrangements are observed in other multi-heme proteins. Striking structural similarities are evident between the tetra-heme core of cyt c554 and hemes 3-6 of HAO, which suggests an evolutionary relationship between these redox partners.


    Organizational Affiliation

    Graduate Option in Biochemistry, California Institute of Technology, Pasadena 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C-554
A
211Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298)Gene Names: cycA1, cycA2, cycA3 (cycA, hcy, cycA, cycA)
Find proteins for Q57142 (Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298))
Go to UniProtKB:  Q57142
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.200α = 90.00
b = 68.200β = 90.00
c = 168.833γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance