Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 170.10 kDa 
• Atom Count: 10788 
• Residue Count: 1377 
• Unique protein chains: 1

2VA1

Crystal structure of UMP kinase from Ureaplasma parvum

• DOI: 10.2210/pdb2VA1/pdb

• Classification: TRANSFERASE
• Organism(s): Ureaplasma parvum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-08-28 Released: 2007-09-18 
• Deposition Author(s): Egeblad-Welin, L., Welin, M., Wang, L., Eriksson, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.285 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 

Literature

Structural and Functional Investigations of Ureaplasma Parvum Ump Kinase - a Potential Antibacterial Drug Target

Egeblad-Welin, L., Welin, M., Wang, L., Eriksson, S.

(2007) FEBS J 274: 6403

• PubMed: 18021254 
• DOI: 10.1111/j.1742-4658.2007.06157.x
• Primary Citation of Related Structures:  
  2VA1


• PubMed Abstract: 
  

The crystal structure of uridine monophosphate kinase (UMP kinase, UMPK) from the opportunistic pathogen Ureaplasma parvum was determined and showed similar three-dimensional fold as other bacterial and archaeal UMPKs that all belong to the amino acid kinase family. Recombinant UpUMPK exhibited Michaelis-Menten kinetics with UMP, with K(m) and V(max) values of 214 +/- 4 microm and 262 +/- 24 micromol.min(-1).mg(-1), respectively, but with ATP as variable substrate the kinetic analysis showed positive cooperativity, with an n value of 1.5 +/- 0.1. The end-product UTP was a competitive inhibitor against UMP and a noncompetitive inhibitor towards ATP. Unlike UMPKs from other bacteria, which are activated by GTP, GTP had no detectable effect on UpUMPK activity. An attempt to create a GTP-activated enzyme was made using site-directed mutagenesis. The mutant enzyme F133N (F133 corresponds to the residue in Escherichia coli that is involved in GTP activation), with F133A as a control, were expressed, purified and characterized. Both enzymes exhibited negative cooperativity with UMP, and GTP had no effect on enzyme activity, demonstrating that F133 is involved in subunit interactions but apparently not in GTP activation. The physiological role of UpUMPK in bacterial nucleic acid synthesis and its potential as target for development of antimicrobial agents are discussed.

---

Organizational Affiliation: 

Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URIDYLATE KINASE	A, B, C, D, E, F	256	Ureaplasma parvum	Mutation(s): 0  EC: 2.7.4.22 (PDB Primary Data), 2.7.4 (PDB Primary Data)
Find proteins for Q9PPX6 (Ureaplasma parvum serovar 3 (strain ATCC 700970)) Explore Q9PPX6  Go to UniProtKB:  Q9PPX6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A, B, C, D, E, F	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.285 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.753	α = 90
b = 96.552	β = 105.75
c = 96.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-28 
• Released Date: 2007-09-18 
Deposition Author(s): Egeblad-Welin, L., Welin, M., Wang, L., Eriksson, S.

Revision History 

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance