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- PDB-1gph: STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS -

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Basic information

Entry
Database: PDB / ID: 1gph
TitleSTRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS
ComponentsGLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
KeywordsTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / 4 iron, 4 sulfur cluster binding / magnesium ion binding
Similarity search - Function
Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain ...Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / IRON/SULFUR CLUSTER / Amidophosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsSmith, J.L.
CitationJournal: Science / Year: 1994
Title: Structure of the allosteric regulatory enzyme of purine biosynthesis.
Authors: Smith, J.L. / Zaluzec, E.J. / Wery, J.P. / Niu, L. / Switzer, R.L. / Zalkin, H. / Satow, Y.
History
DepositionApr 20, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 21, 2014Group: Structure summary
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
1: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
2: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
3: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
4: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,21316
Polymers202,0294
Non-polymers4,18412
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
1: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
2: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1078
Polymers101,0142
Non-polymers2,0926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-75 kcal/mol
Surface area33170 Å2
MethodPISA
3
3: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
4: GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1078
Polymers101,0142
Non-polymers2,0926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-79 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.800, 75.700, 94.100
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 1 86 / 2: CIS PROLINE - PRO 2 86 / 3: CIS PROLINE - PRO 3 86 / 4: CIS PROLINE - PRO 4 86
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.934886, 0.35078, 0.054242), (0.35078, -0.936406, 0.009834), (0.054242, 0.009834, -0.998479)-3.586, 13.927, 37.839
2given(-0.995331, -0.010925, -0.095902), (-0.010925, -0.974435, 0.224402), (-0.095902, 0.224402, 0.969766)238.007, 52.939, 5.557
3given(-0.939555, -0.339854, 0.04166), (-0.339854, 0.910842, -0.234234), (0.04166, -0.234234, -0.971287)237.795, 47.898, 45.721

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Components

#1: Protein
GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE


Mass: 50507.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / References: UniProt: P00497, amidophosphoribosyltransferase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
Nonpolymer detailsTHE FE ATOMS OF THE [4FE-4S] CLUSTER ARE LIGATED BY CYSTEINE S(GAMMA) ATOMS AS FOLLOWS: FE 1 - SG ...THE FE ATOMS OF THE [4FE-4S] CLUSTER ARE LIGATED BY CYSTEINE S(GAMMA) ATOMS AS FOLLOWS: FE 1 - SG CYS 437; FE 2 - SG CYS 236; FE 3 - SG CYS 440; FE 4 - SG CYS 382. THE AMP MOLECULE THAT IS RESIDUE 467 IS BOUND TO THE SITE WHERE THE SUBSTRATE PRPP IS PRESUMED TO BIND. THE AMP MOLECULE THAT IS RESIDUE 468 IS BOUND BETWEEN SUBUNITS IN WHAT IS PRESUMED TO BE AN ALLOSTERIC REGULATORY SITE.
Sequence detailsTHE STRUCTURE DIFFERS FROM THE DEPOSITED SEQUENCE IN TWO PLACES: 1) AN 11-RESIDUE PROPEPTIDE ...THE STRUCTURE DIFFERS FROM THE DEPOSITED SEQUENCE IN TWO PLACES: 1) AN 11-RESIDUE PROPEPTIDE REMOVED POSTTRANSLATIONALLY IS NOT PRESENT IN THE MATURE PROTEIN OR IN THE CRYSTALS, BUT IS INCLUDED IN THE SWISS-PROT ENTRY. RESIDUE NUMBERS IN THE PDB ENTRY ARE WITH RESPECT TO THE MATURE PROTEIN AND THOSE IN THE SWISS-PROT ENTRY ARE WITH RESPECT TO THE UNPROCESSED PROTEIN (I+11). SEQRES RECORDS IN THIS ENTRY CORRESPOND TO THE SEQUENCE OF MATURE PROTEIN. 2) RESIDUE 402 IS REPORTED FROM SEQUENCING TO BE GLYCINE BUT STRONG ELECTRON DENSITY AT THIS POSITION BRIDGES TO AN ARGININE SIDE CHAIN AND IS BEST FIT WITH A SIDE CHAIN OF THREE-ATOM LENGTH. AN ASPARTATE RESIDUE WAS MODELED INTO THIS DENSITY, REFINED, AND INCLUDED IN THE DEPOSITED MODEL. SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PUR1_BACSU SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLY 413 ASP 1 402 GLY 413 ASP 2 402 GLY 413 ASP 3 402 GLY 413 ASP 4 402

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal grow
*PLUS
pH: 7.9 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-8 mg/mlprotein11
250 mMTris-HCl11
33-4 mM11MgCl2
45 mMDTE11
52 mMAMP11
612-13 %(w/v)PEG800011
710 mM12MgCl2
85 mMDTE12
92 mMAMP12
1015 %PEG800012
1150 mMTris-HCl12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 41267 / % possible obs: 90.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 37670
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14156 0 216 0 14372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.3
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: 0.182 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.3

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