PDBsum entry 1ffv

Hydrolase

PDB id: 1ffv

Contents

Protein chains

155 a.a. *

797 a.a. *

287 a.a. *

Ligands

FES ×4

PCD ×2

FAD ×2

Waters ×1607

* Residue conservation analysis

PDB id:

1ffv

Name:

Hydrolase

Title:

Carbon monoxide dehydrogenase from hydrogenophaga pseudoflava

Structure:

Cuts, iron-sulfur protein of carbon monoxide dehydrogenase. Chain: a, d. Cutl, molybdoprotein of carbon monoxide dehydrogenase. Chain: b, e. Cutm, flavoprotein of carbon monoxide dehydrogenase. Chain: c, f

Source:

Hydrogenophaga pseudoflava. Organism_taxid: 47421. Organism_taxid: 47421

Biol. unit:

Hexamer (from PQS)

Resolution:

2.25Å R-factor: 0.209 R-free: 0.237

Authors:

P.Haenzelmann,H.Dobbek,L.Gremer,R.Huber,O.Meyer

Key ref:

P.Hänzelmann et al. (2000). The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase. J Mol Biol, 301, 1221-1235. PubMed id: 10966817 DOI: 10.1006/jmbi.2000.4023

Date:

26-Jul-00 Release date: 15-Sep-00

Protein chains

P19915  (DCMS_HYDPS) -  Carbon monoxide dehydrogenase small chain from Hydrogenophaga pseudoflava

Seq: 163 a.a.

Struc: 155 a.a.*

Protein chains

P19913  (DCML_HYDPS) -  Carbon monoxide dehydrogenase large chain from Hydrogenophaga pseudoflava

Seq: 803 a.a.

Struc: 797 a.a.*

Protein chains

P19914  (DCMM_HYDPS) -  Carbon monoxide dehydrogenase medium chain from Hydrogenophaga pseudoflava

Seq: 287 a.a.

Struc: 287 a.a.*

* PDB and UniProt seqs differ at 17 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.1.2.5.3 - aerobic carbon monoxide dehydrogenase.
• Reaction: CO + a quinone + H2O = a quinol + CO2
• Cofactor: Cu cation; FAD; Iron-sulfur; Molybdenum atom; Molybdopterin

Cu cation FAD (Bound ligand (Het Group name = FAD) corresponds exactly) Iron-sulfur Molybdenum atom Molybdopterin (Bound ligand (Het Group name = PCD) matches with 50.00% similarity)

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

reference

DOI no: 10.1006/jmbi.2000.4023

J Mol Biol 301:1221-1235 (2000)

PubMed id: 10966817

The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.

P.Hänzelmann, H.Dobbek, L.Gremer, R.Huber, O.Meyer.

ABSTRACT

Crystal structures of carbon monoxide dehydrogenase (CODH), a seleno-molybdo-iron-sulfur flavoprotein from the aerobic carbon monoxide utilizing carboxidotrophic eubacterium Hydrogenophaga pseudoflava, have been determined from the enzyme synthesized at high (Mo(plus) CODH) and low intracellular molybdenum content (Mo(minus) CODH) at 2.25 A and 2.35 A resolution, respectively. The structures were solved by Patterson search methods utilizing the enzyme from Oligotropha carboxidovorans as the initial model. The CODHs from both sources are structurally very much conserved and show the same overall fold, architecture and arrangements of the molybdopterin-cytosine dinucleotide-type of molybdenum cofactor, the type I and type II [2Fe-2S] clusters and the flavin-adenine dinucleotide. Unlike the CODH from O. carboxidovorans, the enzyme from H. pseudoflava reveals a unique post-translationally modified C(gamma)-hydroxy-Arg384 residue which precedes the catalytically essential S-selanyl-Cys385 in the active-site loop. In addition, the Trp193 which shields the isoalloxazine ring of the flavin-adenine dinucleotide in the M subunit of the H. pseudoflava CODH is a Tyr193 in the O. carboxidovorans CODH. The hydrogen bonding interaction pattern of the molybdenum cofactor involves 27 hydrogen bonds with the surrounding protein. Of these, eight are with the cytosine moiety, eight with the pyrophosphate, six with the pyranopterin, and five with the ligands of the Mo ion. The structure of the catalytically inactive Mo(minus) CODH indicates that an intracellular Mo-deficiency affects exclusively the active site of the enzyme as an incomplete non-functional molybdenum cofactor was synthesized. The 5'-CDP residue was present in Mo(minus) CODH, whereas the Mo-pyranopterin moiety was absent. In Mo(plus) CODH the selenium faces the Mo ion and flips away from the Mo site in Mo(minus) CODH. The different side-chain conformations of the active-site residues S-selanyl-Cys385 and Glu757 in Mo(plus) and Mo(minus) CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues.

Selected figure(s)

Figure 2.
Figure 2. The fold of the L-subunit of the Moplus CODH species. (a) The C-terminal domain (residues 440 to 803). (b) The N-terminal domain (residues 7 to 435). Helices are shown in red, b-sheets in yellow and loops in green. Colour coding of the Moco atoms is as follows: C, green; N, blue; O, red; P, pink. The structure representations were created as in Figure 1.

Figure 3.
Figure 3. Representation of the active sites of the Moplus or the Mominus CODH species. (a) Moplus CODH. The Mo ion is complexed by the enedithiolate group of MCD. It has one hydroxy and two oxo ligands in the first coordination sphere. In the second coordination sphere are the residues Gln237, C^g-hydroxy-Arg384, S-selanyl-Cys385, Gly563 (not shown for reasons of clarity) and Glu757. Hydrogen bonds are shown as broken lines. Colour coding of the Moco atoms is as follows: C, green; Mo, grey; N, blue; O, red; P, pink; S, yellow; Se, orange. (b) Superposition of the active sites of the Moplus and the Mominus CODH species. The active sites of the Moplus or Mominus CODH species are drawn in green and red, respectively. The structure representations were created as in Figure 1.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 1221-1235) copyright 2000.

Figures were selected by an automated process.