PDBsum entry 1qdb

Oxidoreductase

PDB id: 1qdb

Contents

Protein chains

473 a.a. *

Ligands

SO4 ×9

HEC ×15

Metals

_CA ×3

Waters ×1485

* Residue conservation analysis

PDB id:

1qdb

Name:

Oxidoreductase

Title:

CytochromE C nitrite reductase

Structure:

CytochromE C nitrite reductase. Chain: a, b, c

Source:

Sulfurospirillum deleyianum. Organism_taxid: 65553. Cellular_location: periplasm

Biol. unit:

Dimer (from PDB file)

Resolution:

1.90Å R-factor: 0.184 R-free: 0.220

Authors:

O.Einsle,A.Messerschmidt,P.Stach,R.Huber,P.M.H.Kroneck

Key ref:

O.Einsle et al. (1999). Structure of cytochrome c nitrite reductase. Nature, 400, 476-480. PubMed id: 10440380 DOI: 10.1038/22802

Date:

19-May-99 Release date: 18-Aug-99

Protein chains

Q9Z4P4  (NRFA_SULDE) -  Cytochrome c-552 from Sulfurospirillum deleyianum

Seq: 514 a.a.

Struc: 473 a.a.

Enzyme reactions

• Enzyme class: E.C.1.7.2.2 - nitrite reductase (cytochrome; ammonia-forming).
• Reaction: 6 Fe(III)-[cytochrome c] + NH4⁺ + 2 H2O = 6 Fe(II)-[cytochrome c] + nitrite + 8 H⁺
• Cofactor: Ca(2+); Heme

Ca(2+) Heme (Bound ligand (Het Group name = HEC) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/22802

Nature 400:476-480 (1999)

PubMed id: 10440380

Structure of cytochrome c nitrite reductase.

O.Einsle, A.Messerschmidt, P.Stach, G.P.Bourenkov, H.D.Bartunik, R.Huber, P.M.Kroneck.

ABSTRACT

The enzyme cytochrome c nitrite reductase catalyses the six-electron reduction of nitrite to ammonia as one of the key steps in the biological nitrogen cycle, where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification. Here we report on the crystal structure of this enzyme from the microorganism Sulfurospirillum deleyianum, which we solved by multiwavelength anomalous dispersion methods. We propose a reaction scheme for the transformation of nitrite based on structural and spectroscopic information. Cytochrome c nitrite reductase is a functional dimer, with 10 close-packed haem groups of type c and an unusual lysine-coordinated high-spin haem at the active site. By comparing the haem arrangement of this nitrite reductase with that of other multihaem cytochromes, we have been able to identify a family of proteins in which the orientation of haem groups is conserved whereas structure and function are not.

Selected figure(s)

Figure 1.
Figure 1: The nitrite reductase dimer. A front view with the dimer axis orientated vertically, the five haems in each monomer (white), the Ca^2+ ions (grey) and Lys 133 which coordinates the active-site iron atom (yellow). In the right monomer, the protein chain is coloured blue from the amino-terminal end to red at the carboxy-terminal end, in the left monomer according to secondary structure. The dimer interface is dominated by three long -helices per monomer. All haems in the dimer are covalently attached to the protein and their iron atoms are arranged almost in a plane parallel to the plane of the paper.

Figure 2.
Figure 2: Haem arrangement. The overall orientation corresponds to Fig. 1, with the active site located at haem 1 and the line indicating the dimer interface. Haems in the left monomer are numbered according to their attachment to the protein chain. In the right monomer, the Fe–Fe distances (å) between the haems are given. Haems 5 interact across the dimer interface with a distance closer than haems 2 and 3 within each monomer.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 400, 476-480) copyright 1999.

Figures were selected by an automated process.