1PYM

PHOSPHOENOLPYRUVATE MUTASE FROM MOLLUSK IN WITH BOUND MG2-OXALATE

• PDB DOI: https://doi.org/10.2210/pdb1PYM/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): Mytilus edulis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-02-25 Released: 1999-07-21 
• Deposition Author(s): Huang, K., Li, Z., Herzberg, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.188 

Literature

Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate.

Huang, K., Li, Z., Jia, Y., Dunaway-Mariano, D., Herzberg, O.

(1999) Structure 7: 539-548

• PubMed: 10378273 
• DOI: https://doi.org/10.1016/s0969-2126(99)80070-7
• Primary Citation of Related Structures:  
  1PYM


• PubMed Abstract: 
  

  Phosphonate compounds are important secondary metabolites in nature and, when linked to macromolecules in eukaryotes, they might play a role in cell signaling. The first obligatory step in the biosynthesis of phosphonates is the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-pyr), a reaction that is catalyzed by PEP mutase. The PEP mutase functions as a tetramer and requires magnesium ions (Mg2+).

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 66.79 kDa 
• Atom Count: 5,158 
• Modelled Residue Count: 580 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PHOSPHOENOLPYRUVATE MUTASE)	A, B	295	Mytilus edulis	Mutation(s): 0  EC: 5.4.2.9
UniProt
Find proteins for P56839 (Mytilus edulis) Explore P56839  Go to UniProtKB:  P56839

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXL	C [auth A], E [auth B]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.188 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.4	α = 90
b = 131.1	β = 90
c = 90.9	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
MLPHARE	phasing
DM	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-21 
Deposition Author(s): Huang, K., Li, Z., Herzberg, O.

Revision History  

• Version 1.0: 1999-07-21
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations