PDBsum entry 1r7h

Electron transport

PDB id: 1r7h

Contents

Protein chains

74 a.a. *

Waters ×37

* Residue conservation analysis

PDB id:

1r7h

Name:

Electron transport

Title:

Nrdh-redoxin of corynebacterium ammoniagenes forms a domain-swapped dimer

Structure:

Nrdh-redoxin. Chain: a, b. Engineered: yes

Source:

Corynebacterium ammoniagenes. Organism_taxid: 1697. Gene: nrdh. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.69Å R-factor: 0.245 R-free: 0.288

Authors:

M.Stehr,Y.Lindqvist

Key ref:

M.Stehr and Y.Lindqvist (2004). NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer. Proteins, 55, 613-619. PubMed id: 15103625 DOI: 10.1002/prot.20126

Date:

21-Oct-03 Release date: 04-May-04

Protein chains

O69271  (O69271_CORAM) -  Glutaredoxin-like protein NrdH from Corynebacterium ammoniagenes

Seq: 75 a.a.

Struc: 74 a.a.

DOI no: 10.1002/prot.20126

Proteins 55:613-619 (2004)

PubMed id: 15103625

NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer.

M.Stehr, Y.Lindqvist.

ABSTRACT

NrdH-redoxins constitute a family of small redox proteins, which contain a conserved CXXC sequence motif, and are characterized by a glutaredoxin-like amino acid sequence but a thioredoxin-like activity profile. Here we report the structure of Corynebacterium ammoniagenes NrdH at 2.7 A resolution, determined by molecular replacement using E. coli NrdH as model. The structure is the first example of a domain-swapped dimer from the thioredoxin family. The domain-swapped structure is formed by an inter-chain two-stranded anti-parallel beta-sheet and is stabilized by electrostatic interactions at the dimer interface. Size exclusion chromatography, and MALDI-ESI experiments revealed however, that the protein exists as a monomer in solution. Similar to E. coli NrdH-redoxin and thioredoxin, C. ammoniagenes NrdH-redoxin has a wide hydrophobic pocket at the surface that could be involved in binding to thioredoxin reductase. However, the loop between alpha2 and beta3, which is complementary to a crevice in the reductase in the thioredoxin-thioredoxin reductase complex, is the hinge for formation of the swapped dimer in C. ammoniagenes NrdH-redoxin. C. ammoniagenes NrdH-redoxin has the highly conserved sequence motif W61-S-G-F-R-P-[DE]67 which is unique to the NrdH-redoxins and which determines the orientation of helix alpha3. An extended hydrogen-bond network, similar to that in E. coli NrdH-redoxin, determines the conformation of the loop formed by the conserved motif.

Selected figure(s)

Figure 1.
Figure 1. Schematic drawings of the three-dimensional structure of C. ammoniagenes NrdH. The nomenclature of Martin (1995)[7] was used for the helices and sheets and does not include the -sheet of the dimer-interface. The redox active cysteine residues at the N-terminal of helix 1 are shown as ball-and-stick models. A: Closed monomer. B: Open monomer. C: Domain-swapped dimer, colored according to the B-factors from light blue (20 Å^2) to red (45 Å^2) as indicated on the reference bar. D: surface representation of the domain-swapped dimer. The surface was calculated with program MolMol[22] using a solvent radius of 1.4 Å and colored according to the electrostatic potential, calculated with the program s simplecharge option.

Figure 2.
Figure 2. Hydrogen-bond networks in the domain-swapped NrdH dimer. A: The dimer interface. The -sheet of the interface is formed by the residues 48-50 of both domain-swapped monomers. The residues D37*, R40*, D40, and D41 of both 2 helices form a hydrogen-bond network. The molecule has the same orientation as in Figure 1(A-D). B: View of the hydrogen-bond network in the structure of C. ammonigenes NrdH formed by the highly conserved WSGRFP sequence motif. Hydrogen bonds are drawn as dashed lines.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 55, 613-619) copyright 2004.

Figures were selected by an automated process.