PDBsum entry 3duv

Transferase

PDB id: 3duv

Contents

Protein chains

238 a.a. *

254 a.a. *

Ligands

KDO ×2

P4C

Waters ×162

* Residue conservation analysis

PDB id:

3duv

Name:

Transferase

Title:

Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from haemophilus influenzae complexed with the substrate 3-deoxy- manno-octulosonate in the-configuration

Structure:

3-deoxy-manno-octulosonate cytidylyltransferase. Chain: a, b. Synonym: cmp-kdo synthetase, cmp-2-keto-3-deoxyoctulosonic acid synthetase, cks. Engineered: yes

Source:

Haemophilus influenzae. Organism_taxid: 727. Gene: kdsb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.177 R-free: 0.236

Authors:

H.J.Yoon,M.J.Ku,B.Mikami,S.W.Suh

Key ref:

H.J.Yoon et al. (2008). Structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the beta-configuration. Acta Crystallogr D Biol Crystallogr, 64, 1292-1294. PubMed id: 19018107 DOI: 10.1107/S0907444908036342

Date:

18-Jul-08 Release date: 09-Dec-08

Protein chain

P44490  (KDSB_HAEIN) -  3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 254 a.a.

Struc: 238 a.a.

Protein chain

P44490  (KDSB_HAEIN) -  3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 254 a.a.

Struc: 254 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.7.7.38 - 3-deoxy-manno-octulosonate cytidylyltransferase.
• Reaction: 3-deoxy-alpha-D-manno-oct-2-ulosonate + CTP = CMP-3-deoxy-beta-D-manno- octulosonate + diphosphate

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

Added reference

DOI no: 10.1107/S0907444908036342

Acta Crystallogr D Biol Crystallogr 64:1292-1294 (2008)

PubMed id: 19018107

Structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the beta-configuration.

H.J.Yoon, M.J.Ku, B.Mikami, S.W.Suh.

ABSTRACT

The enzyme 3-deoxy-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase; CKS) catalyzes the activation of 3-deoxy-D-manno-octulosonate (or 2-keto-3-deoxy-manno-octonic acid; KDO) by forming CMP-KDO. CKS is unique to Gram-negative bacteria and is an attractive target for the development of antibacterial agents. The crystal structure of CKS from Haemophilus influenzae in complex with the substrate KDO has been determined at 2.30 A resolution by combining single-wavelength anomalous diffraction and molecular-replacement methods. The two monomers in the asymmetric unit differ in the conformation of their C-terminal alpha-helix (Ala230-Asn254). The KDO bound to the active site exists as the beta-pyranose form in the (5)C(2) chair conformation. The structure of CKS from H. influenzae in complex with KDO will be useful in structure-based inhibitor design.

Selected figure(s)

Figure 1.
Figure 1 Structure of H. influenzae CKS bound with the substrate KDO. (a) Ribbon diagram of the dimer in stereo. Chains A and B are coloured green and cyan, respectively. The C-terminal -helical region is highlighted in magenta and orange for chains A and B, respectively, to show the different conformations. These figures were drawn using the program PyMOL (http://www.pymol.org/ ). (b) Stereoview of KDO bound to the active site in chain A. The (F[o] - F[c]) OMIT electron-density map (coloured blue) contoured at 1.0 is superimposed on the refined model. KDO (red) is shown as a stick model and the bound water molecules are shown as red balls. The magenta dotted lines indicate hydrogen bonds. The arrow indicates the anomeric centre at C2 of KDO.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 1292-1294) copyright 2008.