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- PDB-2h31: Crystal structure of human PAICS, a bifunctional carboxylase and ... -

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Basic information

Entry
Database: PDB / ID: 2h31
TitleCrystal structure of human PAICS, a bifunctional carboxylase and synthetase in purine biosynthesis
ComponentsMultifunctional protein ADE2
KeywordsLIGASE / LYASE / alpha-beta-alpha
Function / homology
Function and homology information


phosphoribosylaminoimidazole carboxylase / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process ...phosphoribosylaminoimidazole carboxylase / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cadherin binding / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Class II PurE / : / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / PurE domain / AIR carboxylase / AIR carboxylase ...Class II PurE / : / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBON DIOXIDE / Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLi, S.-X. / Tong, Y.-P. / Xie, X.-C. / Li, S.-G. / Bi, R.-C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Octameric structure of the human bifunctional enzyme PAICS in purine biosynthesis.
Authors: Li, S.X. / Tong, Y.P. / Xie, X.C. / Wang, Q.H. / Zhou, H.N. / Han, Y. / Zhang, Z.Y. / Gao, W. / Li, S.G. / Zhang, X.C. / Bi, R.C.
History
DepositionMay 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
A: Multifunctional protein ADE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5072
Polymers47,4631
Non-polymers441
Water41423
1
A: Multifunctional protein ADE2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)380,05916
Polymers379,7078
Non-polymers3528
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area40220 Å2
ΔGint-231 kcal/mol
Surface area116570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.666, 133.666, 60.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsThe biological assembly is a octamer generated from the monomer in the asymmetric unit by the operations: -x,-y,z and -y,x,z and y,-x,z and -x,y,-z and x,-y,-z and y,x,-z and -y,-x,-z.

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Components

#1: Protein Multifunctional protein ADE2 / Phosphoribosylaminoimidazole-succinocarboxamide synthase / Phosphoribosylaminoimidazole carboxylase


Mass: 47463.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAICS, ADE2, AIRC, PAIS / Production host: Escherichia coli (E. coli)
References: UniProt: P22234, phosphoribosylaminoimidazolesuccinocarboxamide synthase, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0M succinic acid pH 7.0, 0.1M hepes pH 7.0, 0.5%(w/v) PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9780, 0.9796, 0.9643
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2005
RadiationMonochromator: SGM-TRAIN / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97961
30.96431
ReflectionResolution: 2.8→50 Å / Num. all: 14136 / Num. obs: 14136 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.9

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Processing

Software
NameClassification
ADSCdata collection
HKL-2000data reduction
SOLVEphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.287 1375 RANDOM
Rwork0.241 --
all0.245 14136 -
obs0.245 12062 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 3 23 3004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.534

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