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- PDB-1pl0: Crystal structure of human ATIC in complex with folate-based inhi... -

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Basic information

Entry
Database: PDB / ID: 1pl0
TitleCrystal structure of human ATIC in complex with folate-based inhibitor, BW2315U89UC
ComponentsBifunctional purine biosynthesis protein PURH
KeywordsTRANSFERASE / HYDROLASE / human ATIC / AICAR / AICAR transformylase / IMP Cyclohydrolase / xanthosine monophosphate / folate-based inhibitor / BW2315U89UC
Function / homology
Function and homology information


phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / brainstem development / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 ...phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / brainstem development / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 / 'de novo' IMP biosynthetic process / nucleobase-containing compound metabolic process / dihydrofolate metabolic process / animal organ regeneration / tetrahydrofolate biosynthetic process / cerebellum development / cerebral cortex development / Signaling by ALK fusions and activated point mutants / cadherin binding / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily ...Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / Chem-BW2 / : / XANTHOSINE-5'-MONOPHOSPHATE / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCheong, C.G. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structures of Human Bifunctional Enzyme Aminoimidazole-4-carboxamide Ribonucleotide Transformylase/IMP Cyclohydrolase in Complex with Potent Sulfonyl-containing Antifolates.
Authors: Cheong, C.G. / Wolan, D.W. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A.
History
DepositionJun 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN PART OF THE BW2 LIGAND IS MISSING DUE TO LACK OF ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
C: Bifunctional purine biosynthesis protein PURH
D: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,65515
Polymers258,7754
Non-polymers2,88011
Water6,990388
1
A: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6597
Polymers129,3872
Non-polymers1,2715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-67 kcal/mol
Surface area42530 Å2
MethodPISA
2
C: Bifunctional purine biosynthesis protein PURH
D: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9978
Polymers129,3872
Non-polymers1,6096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-69 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.120, 92.970, 178.490
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological unit is a homodimer

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Bifunctional purine biosynthesis protein PURH / ATIC


Mass: 64693.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (AICAR TRANSFORMYLASE) AND IMP CYCLOHYDROLASE (INOSINICASE) (IMP SYNTHETASE)
Source: (gene. exp.) Homo sapiens (human) / Gene: ATIC / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3
References: UniProt: P31939, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase

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Non-polymers , 5 types, 399 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#4: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR


Mass: 338.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N4O8P
#5: Chemical ChemComp-BW2 / N-(4-{[(2-AMINO-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)AMINO]SULFONYL}BENZOYL)GLUTAMIC ACID / BW2315U89UC


Mass: 489.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N5O8S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: polyethylene glycol 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 106 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 71039 / % possible obs: 91.3 % / Redundancy: 2.7 % / Rsym value: 0.124 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 3597 / Rsym value: 0.659 / % possible all: 92.3

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G8M

1g8m


Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 3426 random 5%
Rwork0.213 --
obs-64075 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17397 0 168 388 17953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.39

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