Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 54.12 kDa 
• Atom Count: 4230 
• Modelled Residue Count: 486 
• Deposited Residue Count: 490 
• Unique protein chains: 1

1H7E

The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, Apo-enzyme

• PDB DOI: 10.2210/pdb1H7E/pdb

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-07-06 Released: 2001-09-13 
• Deposition Author(s): Jelakovic, S., Schulz, G.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.209 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 

Literature

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

• PubMed: 11545592 
• DOI: 10.1006/jmbi.2001.4948
• Primary Citation of Related Structures:  
  1H7E, 1H7F, 1H7G, 1H7H, 1H7T


• PubMed Abstract: 
  

The enzyme CMP-Kdo synthetase (CKS) catalyzes the activation of the sugar Kdo (2-keto-3-deoxy-manno-octonic acid) by forming a monophosphate diester. CKS is a pharmaceutical target because CMP-Kdo is used in the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have refined the structure of the unligated capsule-specific CKS from Escherichia coli at 1.8 A resolution (1 A=0.1 nm) and we have established the structures of its complexes with the substrate CTP, with CDP and CMP as well as with the product analog CMP-NeuAc (CMP-sialate) by X-ray diffraction analyses at resolutions between 2.1 A and 2.5 A. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold, whereas the C-terminal domains form the dimer interface. The observed binding geometries together with the amino acid variabilities during evolution and the locations of a putative Mg(2+) and of a very strongly bound water molecule suggest a pathway for the catalysis. The N-terminal domain shows sequence homology with the CMP-NeuAc synthetases. Moreover, the chain fold and the substrate-binding position of CKS resemble those of other enzymes processing nucleotide-sugars.

---

Related Citations: 

• 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, Albertstr. 21, Freiburg im Breisgau, Germany, 79104.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE	A, B	245	Escherichia coli	Mutation(s): 0  Gene Names: kpsU EC: 2.7.7.38
UniProt
Find proteins for P42216 (Escherichia coli) Explore P42216  Go to UniProtKB:  P42216

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.209 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.1	α = 90
b = 133.8	β = 102.57
c = 48.48	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-06 
• Released Date: 2001-09-13 
Deposition Author(s): Jelakovic, S., Schulz, G.E.

Revision History  

• Version 1.0: 2001-09-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection