PDBsum entry 2c8v

Oxidoreductase

PDB id: 2c8v

Contents

Protein chain

272 a.a. *

Ligands

FES ×2

ATP

Metals

_MG

Waters ×99

* Residue conservation analysis

PDB id:

2c8v

Name:

Oxidoreductase

Title:

Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: structural characterization of the nitrogenase fe protein leu127 deletion variant with bound mgatp

Structure:

Nitrogenase iron protein 1. Chain: a. Synonym: nitrogenase component ii, nitrogenase reductase, nifh, av2, nitrogenase fe protein 1. Ec: 1.18.6.1

Source:

Azotobacter vinelandii. Organism_taxid: 354

Resolution:

2.50Å R-factor: 0.238 R-free: 0.279

Authors:

S.Sen,A.Krishnakumar,J.Mcclead,M.K.Johnson,L.C.Seefeldt,R.K.Szilagyi, J.W.Peters

Key ref:

S.Sen et al. (2006). Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP. J Inorg Biochem, 100, 1041-1052. PubMed id: 16616373

Date:

08-Dec-05 Release date: 01-Jun-06

Protein chain

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

Seq: 290 a.a.

Struc: 272 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⁺

N2 (Bound ligand (Het Group name = ATP) corresponds exactly) + 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

J Inorg Biochem 100:1041-1052 (2006)

PubMed id: 16616373

Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP.

S.Sen, A.Krishnakumar, J.McClead, M.K.Johnson, L.C.Seefeldt, R.K.Szilagyi, J.W.Peters.

ABSTRACT

In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.