PDBsum entry 4ue3

Oxidoreductase

PDB id: 4ue3

Contents

Protein chains

581 a.a.

265 a.a.

Ligands

NFV ×2

SO4 ×4

SF4 ×2

F3S ×2

SF3 ×2

Metals

_MG ×2

_CL ×4

Waters ×1117

PDB id:

4ue3

Name:

Oxidoreductase

Title:

The mechanism of hydrogen activation by nife-hydrogenases and the importance of the active site arginine

Structure:

Hydrogenase-1 large chain. Chain: s, t. Synonym: hyd1, membrane-bound hydrogenase 1 large subunit, hydrogenase. Engineered: yes. Hydrogenase-1 small chain. Chain: l, m. Fragment: catalytic domain, residues 46-372. Synonym: hyd1, membrane-bound hydrogenase 1 small subunit,

Source:

Escherichia coli. Organism_taxid: 562. Strain: mc4100. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.136 R-free: 0.154

Authors:

R.M.Evans,S.A.M.Wehlin,E.Nomerotskaia,F.Sargent,S.B.Carr, S.E.V.Phillips,F.A.Armstrong

Key ref:

R.M.Evans et al. (2016). Mechanism of hydrogen activation by [NiFe] hydrogenases. Nat Chem Biol, 12, 46-50. PubMed id: 26619250 DOI: 10.1038/nchembio.1976

Date:

15-Dec-14 Release date: 24-Dec-14

Protein chains

P0ACD8  (MBHL_ECOLI) -  Hydrogenase-1 large chain from Escherichia coli (strain K12)

Seq: 597 a.a.

Struc: 581 a.a.*

Protein chains

P69739  (MBHS_ECOLI) -  Hydrogenase-1 small chain from Escherichia coli (strain K12)

Seq: 372 a.a.

Struc: 265 a.a.

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

Enzyme reactions

• Enzyme class: Chains L, M, S, T: E.C.1.12.99.6 - hydrogenase (acceptor).
• Reaction: H2 + A = AH2
• Cofactor: Iron-sulfur; Ni(2+)

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

Key reference

DOI no: 10.1038/nchembio.1976

Nat Chem Biol 12:46-50 (2016)

PubMed id: 26619250

Mechanism of hydrogen activation by [NiFe] hydrogenases.

R.M.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.Phillips, F.A.Armstrong.

ABSTRACT

The active site of [NiFe] hydrogenases contains a strictly conserved arginine that suspends a guanidine nitrogen atom <4.5 Å above the nickel and iron atoms. The guanidine headgroup interacts with the side chains of two conserved aspartic acid residues to complete an outer-shell canopy that has thus far proved intractable to investigation by site-directed mutagenesis. Using hydrogenase-1 from Escherichia coli, the strictly conserved residues R509 and D574 have been replaced by lysine (R509K) and asparagine (D574N) and the highly conserved D118 has been replaced by alanine (D118A) or asparagine (D118N/D574N). Each enzyme variant is stable, and their [(RS)2Niμ(SR)2Fe(CO)(CN)2] inner coordination shells are virtually unchanged. The R509K variant had >100-fold lower activity than native enzyme. Conversely, the variants D574N, D118A and D118N/D574N, in which the position of the guanidine headgroup is retained, showed 83%, 26% and 20% activity, respectively. The special kinetic requirement for R509 implicates the suspended guanidine group as the general base in H2 activation by [NiFe] hydrogenases.