1P9O | pdb_00001p9o

Crystal Structure of Phosphopantothenoylcysteine Synthetase

• PDB DOI: https://doi.org/10.2210/pdb1P9O/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-12 Released: 2003-09-02 
• Deposition Author(s): Manoj, N., Strauss, E., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.

Manoj, N., Strauss, E., Begley, T.P., Ealick, S.E.

(2003) Structure 11: 927-936

• PubMed: 12906824 
• DOI: https://doi.org/10.1016/s0969-2126(03)00146-1
• Primary Citation Related Structures: 
  1P9O


• PubMed Abstract: 
  

  The structure of human phosphopantothenoylcysteine (PPC) synthetase was determined at 2.3 A resolution. PPC synthetase is a dimer with identical monomers. Some features of the monomer fold resemble a group of NAD-dependent enzymes, while other features resemble the ribokinase fold. The ATP, phosphopantothenate, and cysteine binding sites were deduced from modeling studies. Highly conserved ATP binding residues include Gly43, Ser61, Gly63, Gly66, Phe230, and Asn258. Highly conserved phosphopantothenate binding residues include Asn59, Ala179, Ala180, and Asp183 from one monomer and Arg55' from the adjacent monomer. The structure predicts a ping pong mechanism with initial formation of an acyladenylate intermediate, followed by release of pyrophosphate and attack by cysteine to form the final products PPC and AMP.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

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: 68.52 kDa 
• Atom Count: 4,214 
• Modeled Residue Count: 549 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantothenoylcysteine synthetase	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: coaB EC: 6.3.2.5 (PDB Primary Data), 6.3.2.51 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAB8 (Homo sapiens) Explore Q9HAB8  Go to UniProtKB:  Q9HAB8
PHAROS:  Q9HAB8 GTEx:  ENSG00000127125

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.16	α = 90
b = 73.16	β = 90
c = 281.83	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-02 
Deposition Author(s): Manoj, N., Strauss, E., Begley, T.P., Ealick, S.E.

Revision History  

• Version 1.0: 2003-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description