1HMP | pdb_00001hmp

THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH BOUND GMP

• PDB DOI: https://doi.org/10.2210/pdb1HMP/pdb

• Classification: TRANSFERASE (GLYCOSYLTRANSFERASE)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1994-06-03 Released: 1995-06-03 
• Deposition Author(s): Eads, J.C., Scapin, G., Xu, Y., Grubmeyer, C., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP.

Eads, J.C., Scapin, G., Xu, Y., Grubmeyer, C., Sacchettini, J.C.

(1994) Cell 78: 325-334

• PubMed: 8044844 
• DOI: https://doi.org/10.1016/0092-8674(94)90301-8
• Primary Citation Related Structures: 
  1HMP


• PubMed Abstract: 
  

  The crystal structure of HGPRTase with bound GMP has been determined and refined to 2.5 A resolution. The enzyme has a core alpha/beta structure resembling the nucleotide-binding fold of dehydrogenases, and a second lobe composed of residues from the amino and carboxy termini. The GMP molecule binds in an anti conformation in a solvent-exposed cleft of the enzyme. Lys-165, which forms a hydrogen bond to O6 of GMP, appears to be critical for determining the specificity for guanine and hypoxanthine over adenine. The location of active site residues also provides evidence for a possible mechanism for general base-assisted HGPRTase catalysis. A rationalization of the effects on stability and activity of naturally occurring single amino acid mutations of HGPRTase is presented, including a discussion of several mutations at the active site that lead to Lesch-Nyhan syndrome.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461.

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: 49.69 kDa 
• Atom Count: 3,430 
• Modeled Residue Count: 423 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE	A, B	217	Homo sapiens	Mutation(s): 0  EC: 2.4.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for P00492 (Homo sapiens) Explore P00492  Go to UniProtKB:  P00492
PHAROS:  P00492 GTEx:  ENSG00000165704

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	C [auth A], D [auth B]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.5	α = 90
b = 66.45	β = 90
c = 52.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-06-03 
Deposition Author(s): Eads, J.C., Scapin, G., Xu, Y., Grubmeyer, C., Sacchettini, J.C.

Revision History  

• Version 1.0: 1995-06-03
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations