PDBsum entry 2nip

Iron protein

PDB id: 2nip

Contents

Protein chains

286 a.a. *

Ligands

SF4

Waters ×372

* Residue conservation analysis

PDB id:

2nip

Name:

Iron protein

Title:

Nitrogenase iron protein from azotobacter vinelandii

Structure:

Nitrogenase iron protein. Chain: a, b. Ec: 1.18.6.1

Source:

Azotobacter vinelandii. Organism_taxid: 354. Strain: op. Atcc: atcc 13705. Collection: atcc 13705

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.223 R-free: 0.290

Authors:

H.Komiya,M.M.Georgiadis,P.Chakrabarti,D.Woo,J.J.Kornuc,D.C.Rees

Key ref:

J.L.Schlessman et al. (1998). Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. J Mol Biol, 280, 669-685. PubMed id: 9677296 DOI: 10.1006/jmbi.1998.1898

Date:

11-May-98 Release date: 11-Nov-98

Protein chains

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

Seq: 290 a.a.

Struc: 286 a.a.

Enzyme reactions

• Enzyme class: 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: 10.1006/jmbi.1998.1898

J Mol Biol 280:669-685 (1998)

PubMed id: 9677296

Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum.

J.L.Schlessman, D.Woo, L.Joshua-Tor, J.B.Howard, D.C.Rees.

ABSTRACT

The nitrogenase iron (Fe) protein performs multiple functions during biological nitrogen fixation, including mediating the mechanistically essential coupling between ATP hydrolysis and electron transfer to the nitrogenase molybdenum iron (MoFe) protein during substrate reduction, and participating in the biosynthesis and insertion of the FeMo-cofactor into the MoFe-protein. To establish a structural framework for addressing the diverse functions of Fe-protein, crystal structures of the Fe-proteins from Azotobacter vinelandii and Clostridium pasteurianum have been determined at resolutions of 2.2 A and 1.93 A, respectively. These two Fe-proteins are among the more diverse in terms of amino acid sequence and biochemical properties. As described initially for the A. vinelandii Fe-protein in a different crystal form at 2.9 A resolution, each subunit of the dimeric Fe-protein adopts a polypeptide fold related to other mononucleotide-binding proteins such as G-proteins, with the two subunits bridged by a 4Fe:4S cluster. The overall similarities in the subunit fold and dimer arrangement observed in the structures of the A. vinelandii and C. pasteurianum Fe-proteins indicate that they are representative of the conformation of free Fe-protein that is not in complex with nucleotide or the MoFe-protein. Residues in the cluster and nucleotide-binding sites are linked by a network of conserved hydrogen bonds, salt-bridges and water molecules that may conformationally couple these regions. Significant variability is observed in localized regions, especially near the 4Fe:4S cluster and the MoFe-protein binding surface, that change conformation upon formation of the ADP.AlF4- stabilized complex with the MoFe-protein. A core of 140 conserved residues is identified in an alignment of 59 Fe-protein sequences that may be useful for the identification of homologous proteins with functions comparable to that of Fe-protein in non-nitrogen fixing systems.

Selected figure(s)

Figure 4.
Figure 4. (a) A representation of one Fe-protein monomer colored according to rms deviation in C a position, follow- ing superposition of the four AV2 and CP2 subunits. Residues with high rms deviation, such as the C terminus, are indicated in red; regions of strong structural conservation, such as the b-sheet, are indicated in dark blue. (b) A rep- resentation of one Fe-protein monomer colored according to amino acid residue conservation, following alignment of 59 Fe-protein sequences. Residues in red, such as the C terminus, indicate the regions of greatest sequence variability; those in dark blue, such as the 4Fe:4S cluster ligands, P-loop, Switch I and Switch II residues, indicate regions of strongest sequence conservation. In both (a) and (b), the view is from the dimer interface, and Av2 residue numbers are included for reference.

Figure 6.
Figure 6. Structural variability in the subunit-subunit interactions near the 4Fe:4S clusters of CP2 and AV2. Subunit A of each protein is shown in red, and subunit B in green. The 4Fe:4S cluster atoms are colored as in Figure 2. Comp- lementary residues on the opposing subunits have been omitted for ease of viewing. (a) Three intersubunit hydrogen bonds are located near the 4Fe:4S cluster in CP2. (b) Crystal packing forces distort this region in AV2, with the loss of several of these intersubunit interactions. The C terminus of a neighboring molecule (shown in cyan) forms two hydrogen bonds with the 4Fe:4S region of subunit A in AV2 at residues Gly96 and Cys97. Despite this conformation- al alteration near the 4Fe:4S cluster in subunit A, the corresponding region in subunit B is undisturbed.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 280, 669-685) copyright 1998.

Figures were selected by an automated process.