PDBsum entry 4xpi

Oxidoreductase

PDB id: 4xpi

Contents

Protein chains

479 a.a.

522 a.a.

Ligands

HCA ×2

ICS ×2

GOL ×15

1CL ×2

TRS ×2

Metals

_CA ×2

Waters ×921

PDB id:

4xpi

Name:

Oxidoreductase

Title:

Fe protein independent substrate reduction by nitrogenase variants altered in intramolecular electron transfer

Structure:

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

Source:

Azotobacter vinelandii. Organism_taxid: 354. Gene: nifd. Expressed in: azotobacter vinelandii. Expression_system_taxid: 354. Gene: nifk.

Resolution:

1.97Å R-factor: 0.216 R-free: 0.264

Authors:

K.Danyal,A.J.Rasmusen,S.M.Keable,S.Shaw,O.Zadvornyy,S.Duval,D.R.Dean, S.Raugei,J.W.Peters,L.C.Seefeldt

Key ref:

K.Danyal et al. (2015). Fe protein-independent substrate reduction by nitrogenase MoFe protein variants. Biochemistry, 54, 2456-2462. PubMed id: 25831270 DOI: 10.1021/acs.biochem.5b00140

Date:

17-Jan-15 Release date: 14-Oct-15

Protein chains

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

Seq: 492 a.a.

Struc: 479 a.a.

Protein chains

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

Seq: 523 a.a.

Struc: 522 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: 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: 10.1021/acs.biochem.5b00140

Biochemistry 54:2456-2462 (2015)

PubMed id: 25831270

Fe protein-independent substrate reduction by nitrogenase MoFe protein variants.

K.Danyal, A.J.Rasmussen, S.M.Keable, B.S.Inglet, S.Shaw, O.A.Zadvornyy, S.Duval, D.R.Dean, S.Raugei, J.W.Peters, L.C.Seefeldt.

ABSTRACT

The reduction of substrates catalyzed by nitrogenase normally requires nucleotide-dependent Fe protein delivery of electrons to the MoFe protein, which contains the active site FeMo cofactor. Here, it is reported that independent substitution of three amino acids (β-98(Tyr→His), α-64(Tyr→His), and β-99(Phe→His)) located between the P cluster and FeMo cofactor within the MoFe protein endows it with the ability to reduce protons to H2, azide to ammonia, and hydrazine to ammonia without the need for Fe protein or ATP. Instead, electrons can be provided by the low-potential reductant polyaminocarboxylate-ligated Eu(II) (Em values of -1.1 to -0.84 V vs the normal hydrogen electrode). The crystal structure of the β-98(Tyr→His) variant MoFe protein was determined, revealing only small changes near the amino acid substitution that affect the solvent structure and the immediate vicinity between the P cluster and the FeMo cofactor, with no global conformational changes observed. Computational normal-mode analysis of the nitrogenase complex reveals coupling in the motions of the Fe protein and the region of the MoFe protein with these three amino acids, which suggests a possible mechanism for how Fe protein might communicate subtle changes deep within the MoFe protein that profoundly affect intramolecular electron transfer and substrate reduction.