6ACS | pdb_00006acs

poly-cis-prenyltransferase

• PDB DOI: https://doi.org/10.2210/pdb6ACS/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-27 Released: 2018-12-19 
• Deposition Author(s): Ko, T.-P., Chen, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.182 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii

Ko, T.P., Huang, C.H., Lai, S.J., Chen, Y.

(2018) Acta Crystallogr F Struct Biol Commun 74: 765-769

• PubMed: 30511669 
• DOI: https://doi.org/10.1107/S2053230X18012931
• Primary Citation Related Structures: 
  6ACS


• PubMed Abstract: 
  

  Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side chains of the catalytic aspartate and serine. These observations may provide a structural basis for inhibitor design against AbUPPS.

---

Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Department of Biotechnology, HungKuang University, Taichung, Taiwan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 60.21 kDa 
• Atom Count: 4,210 
• Modeled Residue Count: 451 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)	A, B	258	Acinetobacter baumannii	Mutation(s): 0  Gene Names: uppS, ispU, ABUW_1737, AM462_03305, CBI29_02230 EC: 2.5.1.31
UniProt
Find proteins for A0A0D5YHU7 (Acinetobacter baumannii) Explore A0A0D5YHU7  Go to UniProtKB:  A0A0D5YHU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	E [auth A], G [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.182 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.222	α = 90
b = 121.501	β = 90
c = 45.602	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Ko, T.-P., Chen, Y.

---

Funding Organization	Location	Grant Number
	Taiwan	--

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description