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- PDB-1qcz: CRYSTAL STRUCTURE OF E. COLI PURE, AN UNUSUAL MUTASE THAT CATALYZ... -

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Basic information

Entry
Database: PDB / ID: 1qcz
TitleCRYSTAL STRUCTURE OF E. COLI PURE, AN UNUSUAL MUTASE THAT CATALYZES THE CONVERSION OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE (N5-CAIR) TO 4-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE (CAIR) IN THE PURINE BIOSYNTHETIC PATHWAY
ComponentsN5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
KeywordsLYASE / THREE-LAYER (ALPHA-BETA-ALPHA) SANDWICH
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / identical protein binding / cytosol
Similarity search - Function
Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide mutase / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsEalick, S.E. / Mathews, I.I.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.
Authors: Mathews, I.I. / Kappock, T.J. / Stubbe, J. / Ealick, S.E.
#1: Journal: Biochemistry / Year: 1999
Title: Evidence for the Direct Transfer of the Carboxylate of N5-Carboxyaminoimidazole Ribonucleotide (N5-CAIR) to Generate 4-Carboxy-5-Aminoimidazole Ribonucleotide Catalyzed by Escherichia coli purE, an N5-CAIR Mutase
Authors: Meyer, E. / Kappock, T.J. / Osuji, C. / Stubbe, J.
#2: Journal: Biochemistry / Year: 1994
Title: Reactions Catalyzed by 5-Aminoimidazole Ribonucleotide Carboxylases from Escherichia coli Carboxylases from Escherichia coli and Gallus gallus: a Case for Divergent Catalytic Mechanisms
Authors: Firestine, S.M. / Poon, S.W. / Mueller, E.J. / Stubbe, J. / Davisson, V.J.
#3: Journal: Biochemistry / Year: 1994
Title: N5-Carboxyaminoimidazole Ribonucleotide: Evidence for a New Intermediate and Two New Enzymatic Activities in the de novo Purine Biosynthetic Pathway of Escherichia coli
Authors: Mueller, E.J. / Meyer, E. / Rudolph, J. / Davisson, V.J. / Stubbe, J.
#4: Journal: J.Bacteriol. / Year: 1989
Title: Nucleotide Sequence Analysis of the purEK Operon Encoding 5'-Phosphoribosyl-5-Aminoimidazole Carboxylase of Escherichia coli K-12
Authors: Tiedeman, A.A. / Keyhani, J. / Kamholz, J. / 3D Daum, H.A. / Gots, J.S. / Smith, J.M.
#5: Journal: J.Bacteriol. / Year: 1989
Title: Identification and Sequence Analysis of Escherichia coli purE and purK Genes Encoding 5'-Phosphoribosyl-5-Amino-4-Imidazole Carboxylase for de novo Purine Biosynthesis
Authors: Watanabe, W. / Sampei, G. / Aiba, A. / Mizobuchi, K.
History
DepositionMay 10, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE


Theoretical massNumber of molelcules
Total (without water)17,9871
Polymers17,9871
Non-polymers00
Water3,081171
1
A: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
x 8


Theoretical massNumber of molelcules
Total (without water)143,8958
Polymers143,8958
Non-polymers00
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_554-x,y,-z-11
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area32150 Å2
ΔGint-211 kcal/mol
Surface area41210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.040, 113.040, 49.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

21A-367-

HOH

31A-368-

HOH

41A-369-

HOH

51A-370-

HOH

61A-371-

HOH

DetailsThe biological assembly is a octamer which is generated from chain A by the 4-fold and 2-fold symmetry

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Components

#1: Protein N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE / PURE


Mass: 17986.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PNC2 / Gene (production host): PURE / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P09028, UniProt: P0AG18*PLUS, phosphoribosylaminoimidazole carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SUBSTRATE SPECIFICITY OF E. COLI PURE FOR N5-CAIR DIFFERS FROM VERTEBRATE PURE (AIR ...THE SUBSTRATE SPECIFICITY OF E. COLI PURE FOR N5-CAIR DIFFERS FROM VERTEBRATE PURE (AIR CARBOXYLASE, EC 4.1.1.21), WHICH CONVERTS CARBON DIOXIDE AND 5-AMINOIMIDAZOLE RIBONUCLEOTIDE (AIR) INTO 4-CARBOXY-5-AMINOIMIDAZOLE RIBONUCLEOTIDE (CAIR). DETAILS ARE GIVEN IN REFERENCES 1, 2, AND 3. PLANTS, YEASTS, AND PROKARYOTES CONTAIN A SEPAATE ENZYME, PURK (PDB CODE 1B6R), REQUIRED FOR THE PRODUCTION OF N5-CAIR. E. COLI PURE AND PURK ARE NOT SUBUNITS OF A SINGLE AIR CARBOXYLASE ENZYME.
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: 2.22 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG400, TRIS.HCL, MAGNESIUM CHLORIDE, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %PEG4001reservoir
20.2 M1reservoirMgCl2
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 193682 / Num. obs: 25072 / % possible obs: 97.2 % / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.172 / % possible all: 86.7
Reflection
*PLUS
Num. measured all: 193682
Reflection shell
*PLUS
% possible obs: 86.7 %

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Processing

Software
NameVersionClassification
SHAKEmodel building
SnBphasing
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1252 -RANDOM
Rwork0.186 ---
all0.189 25065 --
obs-24987 99.7 %-
Displacement parametersBiso mean: 14.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1882 Å0.1645 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 0 171 1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.361.5
X-RAY DIFFRACTIONx_mcangle_it1.952
X-RAY DIFFRACTIONx_scbond_it2.152
X-RAY DIFFRACTIONx_scangle_it3.182.5
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.262 133 5 %
Rwork0.256 2499 -
obs--83 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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