1F75 | pdb_00001f75

CRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICROCOCCUS LUTEUS B-P 26

• PDB DOI: https://doi.org/10.2210/pdb1F75/pdb

• Classification: TRANSFERASE
• Organism(s): Micrococcus luteus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-06-26 Released: 2001-03-28 
• Deposition Author(s): Fujihashi, M., Zhang, Y.-W., Higuchi, Y., Li, X.-Y., Koyama, T., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor) 
• R-Value Work: 
  0.190 (Depositor) 

Literature

Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase.

Fujihashi, M., Zhang, Y.W., Higuchi, Y., Li, X.Y., Koyama, T., Miki, K.

(2001) Proc Natl Acad Sci U S A 98: 4337-4342

• PubMed: 11287651 
• DOI: https://doi.org/10.1073/pnas.071514398
• Primary Citation Related Structures: 
  1F75


• PubMed Abstract: 
  

  Undecaprenyl diphosphate synthase (UPS) catalyzes the cis-prenyl chain elongation onto trans, trans-farnesyl diphosphate (FPP) to produce undecaprenyl diphosphate (UPP), which is indispensable for the biosynthesis of bacterial cell walls. We report here the crystal structure of UPS as the only three-dimensional structure among cis-prenyl chain elongating enzymes. The structure is classified into a protein fold family and is completely different from the so-called "isoprenoid synthase fold" that is believed to be a common structure for the enzymes relating to isoprenoid biosynthesis. Conserved amino acid residues among cis-prenyl chain elongating enzymes are located around a large hydrophobic cleft in the UPS structure. A structural P-loop motif, which frequently appears in the various kinds of phosphate binding site, is found at the entrance of this cleft. The catalytic site is determined on the basis of these structural features, from which a possible reaction mechanism is proposed.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

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)

Macromolecule Content 

• Total Structure Weight: 58.08 kDa 
• Atom Count: 3,552 
• Modeled Residue Count: 429 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNDECAPRENYL PYROPHOSPHATE SYNTHETASE	A, B	249	Micrococcus luteus	Mutation(s): 1  EC: 2.5.1.31
UniProt
Find proteins for O82827 (Micrococcus luteus) Explore O82827  Go to UniProtKB:  O82827

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.197	α = 90
b = 60.161	β = 105.69
c = 75.703	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-28 
Deposition Author(s): Fujihashi, M., Zhang, Y.-W., Higuchi, Y., Li, X.-Y., Koyama, T., Miki, K.

Revision History  

• Version 1.0: 2001-03-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection