1GQC

THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE COMPLEXED WITH CMP-Kdo at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Catalytic Mechanism of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase as Derived from Complexes with Reaction Educt and Product.

Jelakovic, S.Schulz, G.E.

(2002) Biochemistry 41: 1174

  • Primary Citation of Related Structures:  1GQ9

  • PubMed Abstract: 
  • The activation of the sugar 2-keto-3-deoxy-manno-octonic acid (Kdo) is catalyzed by CMP-Kdo synthetase (EC 2.7.7.38) and results in a monophosphate diester with CMP. The enzyme is a pharmaceutical target because CMP-Kdo is required for the biosynthes ...

    The activation of the sugar 2-keto-3-deoxy-manno-octonic acid (Kdo) is catalyzed by CMP-Kdo synthetase (EC 2.7.7.38) and results in a monophosphate diester with CMP. The enzyme is a pharmaceutical target because CMP-Kdo is required for the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have established the structures of an enzyme complex with the educt CTP and of a complex with the product CMP-Kdo by X-ray diffraction analyses at 100 K, both at 2.6 A resolution. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold with the beta- and gamma-phosphates located at the so-called "PP-loop", whereas the C-terminal domains participate in Kdo binding and in the dimer interface. The unstable nucleotide-sugar CMP-Kdo was produced in a crystal and stabilized by freezing to 100 K. Its formation is accompanied by an induced fit involving mainchain displacements in the 2 A range. The observed binding conformations together with the amino acid conservation pattern during evolution and the putative location of the required Mg(2+) ion suggest a reaction pathway. The enzyme is structurally homologous to the CMP-N-acetylneuraminic acid synthetases in all parts except for the dimer interface. Moreover, the chainfold and the substrate-binding positions resemble those of other enzymes processing nucleotide sugars.


    Related Citations: 
    • The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase and of its Complexes with Substrates and Substrate Analogs
      Jelakovic, S.,Schulz, G.E.
      (2001) J.Mol.Biol. 312: 143
    • The Three-Dimensional Structure of Capsule-Specific Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase from Escherichia Coli
      Jelakovic, S.,Jann, K.,Schulz, G.E.
      (1996) FEBS Lett. 391: 157


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, Freiburg im Breisgau, Germany 79104.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
A, B
245Escherichia coliGene Names: kpsU
EC: 2.7.7.38
Find proteins for P42216 (Escherichia coli)
Go to UniProtKB:  P42216
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C5P
Query on C5P

Download SDF File 
Download CCD File 
B
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
CMK
Query on CMK

Download SDF File 
Download CCD File 
A
CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID
C17 H26 N3 O15 P
YWWJKULNWGRYAS-UOVSKDHASA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.944α = 90.00
b = 130.996β = 102.31
c = 48.148γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance