PDBsum entry 4wcx

Lyase

PDB id: 4wcx

Contents

Protein chains

454 a.a.

Ligands

SF4 ×4

MET

ALA

H2S ×2

SAM

Metals

_NA ×3

_FE

Waters ×814

PDB id:

4wcx

Name:

Lyase

Title:

Crystal structure of hydg: a maturase of the [fefe]-hydrogenase

Structure:

Biotin and thiamin synthesis associated. Chain: a, c. Engineered: yes

Source:

Thermoanaerobacter italicus. Organism_taxid: 580331. Strain: dsm 9252 / ab9. Gene: thit_0582. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.59Å R-factor: 0.181 R-free: 0.213

Authors:

P.C.Dinis,J.E.Harmer,R.C.Driesener,P.L.Roach

Key ref:

P.Dinis et al. (2015). X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly. Proc Natl Acad Sci U S A, 112, 1362-1367. PubMed id: 25605932 DOI: 10.1073/pnas.1417252112

Date:

05-Sep-14 Release date: 04-Feb-15

Protein chains

D3T7F1  (D3T7F1_THEIA) -  Biotin and thiamin synthesis associated from Thermoanaerobacter italicus (strain DSM 9252 / Ab9)

Seq: 466 a.a.

Struc: 454 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.1417252112

Proc Natl Acad Sci U S A 112:1362-1367 (2015)

PubMed id: 25605932

X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly.

P.Dinis, D.L.Suess, S.J.Fox, J.E.Harmer, R.C.Driesener, L.De La Paz, J.R.Swartz, J.W.Essex, R.D.Britt, P.L.Roach.

ABSTRACT

Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN(-) ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (βα)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a μ2-sulfide ion to a mononuclear Fe(2+) center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly.