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- PDB-1hmp: THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSY... -

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Basic information

Entry
Database: PDB / ID: 1hmp
TitleTHE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH BOUND GMP
ComponentsHYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
KeywordsTRANSFERASE (GLYCOSYLTRANSFERASE)
Function / homology
Function and homology information


Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / adenine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine salvage / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation / IMP metabolic process / guanine phosphoribosyltransferase activity ...Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / adenine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine salvage / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation / IMP metabolic process / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / Purine salvage / grooming behavior / GMP salvage / IMP salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / purine ribonucleoside salvage / Azathioprine ADME / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsEads, J.C. / Scapin, G. / Xu, Y. / Grubmeyer, C. / Sacchettini, J.C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP.
Authors: Eads, J.C. / Scapin, G. / Xu, Y. / Grubmeyer, C. / Sacchettini, J.C.
#1: Journal: Biochemistry / Year: 1994
Title: Crystal Structure of Orotate Phosphoribosyltransferase
Authors: Scapin, G. / Grubmeyer, C. / Sacchettini, J.C.
History
DepositionJun 3, 1994Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
B: HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6894
Polymers48,9622
Non-polymers7262
Water1,53185
1
A: HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
B: HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
hetero molecules

A: HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
B: HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3788
Polymers97,9254
Non-polymers1,4534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11460 Å2
ΔGint-66 kcal/mol
Surface area35900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.500, 66.450, 52.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE


Mass: 24481.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE HET GROUP HAS A CHARGE OF 1- AT PH 5.6.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoirprecipitant
30.1 Msodium acetate1reservoirprecipitant
420-24 %PEG40001reservoirprecipitant
51-2 mMdithiothreitol1reservoirprecipitant
60.5 mMEDTA1reservoirprecipitant

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.45 Å / Num. obs: 16428 / % possible obs: 85 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→20 Å / σ(F): 1
Details: A LOOP OF RESIDUES 103 - 121 IN BOTH CHAINS A AND B IS POORLY ORDERED. COORDINATES GIVEN FOR THIS REGION RESULT FROM A TENTATIVE FITTING TO POOR ELECTRON DENSITY AND SHOULD BE TREATED WITH ...Details: A LOOP OF RESIDUES 103 - 121 IN BOTH CHAINS A AND B IS POORLY ORDERED. COORDINATES GIVEN FOR THIS REGION RESULT FROM A TENTATIVE FITTING TO POOR ELECTRON DENSITY AND SHOULD BE TREATED WITH CAUTION. FOR THIS LOOP IN THE SECOND MONOMER, RESIDUES 105 - 108 AND 121 ARE MISSING. SOME RESIDUES IN THIS REGION ARE MODELED AS ALANINE RESIDUES.
RfactorNum. reflection
Rwork0.186 -
obs0.186 14328
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 48 85 3430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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