PDBsum entry 2afh

Oxidoreductase

PDB id: 2afh

Contents

Protein chains

476 a.a. *

522 a.a. *

289 a.a. *

Ligands

HCA ×2

CFN ×2

PGE ×8

CLF ×2

TRS ×2

PG4 ×2

1PE ×2

PEG ×3

P6G

SF4

Metals

_CA ×2

_NA

Waters ×2071

* Residue conservation analysis

PDB id:

2afh

Name:

Oxidoreductase

Title:

Crystal structure of nucleotide-free av2-av1 complex

Structure:

Nitrogenase molybdenum-iron protein. Chain: a, c. Synonym: nitrogenase component i, dinitrogenase. Other_details: alpha chain. Nitrogenase molybdenum-iron protein. Chain: b, d. Synonym: nitrogenase component i, dinitrogenase. Other_details: beta chain. Nitrogenase iron protein 1.

Source:

Azotobacter vinelandii. Organism_taxid: 354. Organism_taxid: 354

Biol. unit:

Hexamer (from PQS)

Resolution:

2.10Å R-factor: 0.172 R-free: 0.221

Authors:

F.A.Tezcan,J.T.Kaiser,D.Mustafi,M.Y.Walton,J.B.Howard,D.C.Rees

Key ref:

F.A.Tezcan et al. (2005). Nitrogenase complexes: multiple docking sites for a nucleotide switch protein. Science, 309, 1377-1380. PubMed id: 16123301 DOI: 10.1126/science.1115653

Date:

25-Jul-05 Release date: 06-Sep-05

Protein chains

P07328  (NIFD_AZOVI) -  Nitrogenase molybdenum-iron protein alpha chain from Azotobacter vinelandii

Seq: 492 a.a.

Struc: 476 a.a.

Protein chains

P07329  (NIFK_AZOVI) -  Nitrogenase molybdenum-iron protein beta chain from Azotobacter vinelandii

Seq: 523 a.a.

Struc: 522 a.a.

Protein chains

P00459  (NIFH1_AZOVI) -  Nitrogenase iron protein 1 from Azotobacter vinelandii

Seq: 290 a.a.

Struc: 289 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.1.18.6.1 - nitrogenase.
• Pathway: Nitrogenase
• Reaction: N2 + 8 reduced [2Fe-2S]-[ferredoxin] + 16 ATP + 16 H2O = H2 + 8 oxidized [2Fe-2S]-[ferredoxin] + 2 NH4⁺ + 16 ADP + 16 phosphate + 6 H⁺
• Cofactor: Iron-sulfur; Vanadium cation or Mo cation

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

reference

DOI no: 10.1126/science.1115653

Science 309:1377-1380 (2005)

PubMed id: 16123301

Nitrogenase complexes: multiple docking sites for a nucleotide switch protein.

F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees.

ABSTRACT

Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.

Selected figure(s)

Figure 2.
Fig. 2. nf-, pcp-, adp-, and alf-[4Fe:4S]-cluster positions relative to the P-cluster and FeMo-cofactor as viewed perpendicular (A) and parallel (B) to the local two-fold axis relating an ß pair of Av1 subunits. The approximate distances shown in the side-view (A) are between the cluster centroids (see also Table 1). The centroid distance between the P-cluster and the FeMo-cofactor is 19.3 Å. The corresponding edge-to-edge [4Fe:4S]-P-cluster distances between the nearest pair of atoms in these structures are 5 Å shorter. The outline of the Av1 surface is shown in coral.

Figure 3.
Fig. 3. Schematic representation of Av1-Av2 docking geometry at different nucleotide states. The species representing the pcp-conformer (dotted lines) is included in both cartoons to illustrate the relative docking positions of Av2 molecules. Taking a reference point near the "top" surface of Av2 (away from the interface with Av1) that is positioned on the two-fold axis at a distance of 35 Å from the [4Fe:4S] cluster of each Av2 dimer (point A: pcp-Av2; point B: nf-Av2; point C, adp-Av2), the displacement between pcp-Av2 and nf-Av2 is 19 Å, and that between pcp-Av2 and the four adp-conformers ranges from 10 to 23 Å.

The above figures are reprinted by permission from the AAAs: Science (2005, 309, 1377-1380) copyright 2005.

Figures were selected by an automated process.