PDBsum entry 1cc9

Ligase

PDB id: 1cc9

Contents

Protein chain

466 a.a.

Ligands

UPM

ADP

Theoretical model

PDB id:

1cc9

Name:

Ligase

Title:

A model structure of udp-n-acetylmuramoyl: l-alanine synthetase (murc) from escherichia coli based on homology and hydrophobic cluster analysis and its validation by amino acid modifications.

Structure:

Udp-n-acetylmuramoyl: l-alanine synthetase). Chain: a. Synonym: murc. Ec: 6.3.2.8

Source:

Escherichia coli. Bacteria. Strain: jm83

Authors:

F.Nosal,R.Legrand,D.A.Rowlands,P.Ferrari,B.Schoot,J.Van Heijenoort

Key ref:

E.Garcin et al. (1999). The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Structure Fold Des, 7, 557-566. PubMed id: 10378275 DOI: 10.1016/S0969-2126(99)80072-0

Date:

04-Mar-99 Release date: 30-Dec-03

Protein chain

P17952  (MURC_ECOLI) -  UDP-N-acetylmuramate--L-alanine ligase

Seq: 491 a.a.

Struc: 466 a.a.

DOI no: 10.1016/S0969-2126(99)80072-0

Structure Fold Des 7:557-566 (1999)

PubMed id: 10378275

The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.

E.Garcin, X.Vernede, E.C.Hatchikian, A.Volbeda, M.Frey, J.C.Fontecilla-Camps.

ABSTRACT

hydrogenases are metalloenzymes that catalyze the reaction H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand. RESULTS: We hydrogenase from Desulfomicrobium baculatum in its reduced, active form. A comparison of active sites of the oxidized, as-prepared, Desulfovibrio gigas and the reduced D. baculatum hydrogenases shows that in the reduced enzyme the nickel-iron distance is 0.4 A shorter than in the oxidized enzyme. In addition, the putative oxo ligand, detected in the as-prepared D. gigas enzyme, is absent from the D. baculatum hydrogenase. We also observe higher-than-average temperature factors for both the active site nickel-selenocysteine ligand and the neighboring Glu18 residue, suggesting that both these moieties are involved in proton transfer between the active site and the molecular surface. Other hydrogenases are the presence of a third cluster found in the D. gigas enzyme, and a putative iron center that substitutes the magnesium ion that has already been hydrogenases. CONCLUSIONS: The heterolytic cleavage of molecular hydrogen seems to be mediated by the nickel center and the selenocysteine residue. Beside modifying the catalytic properties of the enzyme, the selenium ligand might protect the nickel atom from oxidation. We conclude that the putative oxo ligand is a signature of hydrogenases.

Selected figure(s)

Figure 6.
Figure 6. The environment of the putative hydrogen sulfide molecule. Stereoview of the active site and the hydrogen sulfide molecule. The distance between the iron of the active site and the assigned hydrogen sulfide molecule, represented by a dotted line, is 6.7 Å. The hydrogen sulfide molecule is coordinated by residues Thr70L, Ala71L and Asn103L. This figure was made using TURBO-FRODO [42].

The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 557-566) copyright 1999.

Figure was selected by an automated process.