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- PDB-4e2s: Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabid... -

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Basic information

Entry
Database: PDB / ID: 4e2s
TitleCrystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine
ComponentsUreidoglycine aminohydrolase
KeywordsHYDROLASE / bi-cupin / (S)-Ureidoglycine Aminohydrolase / Manganese Binding / Endoplasmic Reticulumn
Function / homology
Function and homology information


(S)-ureidoglycine aminohydrolase / ureidoglycine aminohydrolase activity / ureide catabolic process / allantoin catabolic process / purine nucleobase catabolic process / DNA-binding transcription factor activity / regulation of DNA-templated transcription / endoplasmic reticulum / metal ion binding / cytosol
Similarity search - Function
(S)-ureidoglycine aminohydrolase, C-terminal cupin domain / (S)-ureidoglycine aminohydrolase, N-terminal cupin domain / (S)-ureidoglycine aminohydrolase / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / (2S)-amino(carbamoylamino)ethanoic acid / (S)-ureidoglycine aminohydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsShin, I. / Rhee, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana
Authors: Shin, I. / Percudani, R. / Rhee, S.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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

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Assembly

Deposited unit
A: Ureidoglycine aminohydrolase
B: Ureidoglycine aminohydrolase
C: Ureidoglycine aminohydrolase
D: Ureidoglycine aminohydrolase
E: Ureidoglycine aminohydrolase
F: Ureidoglycine aminohydrolase
G: Ureidoglycine aminohydrolase
H: Ureidoglycine aminohydrolase
I: Ureidoglycine aminohydrolase
J: Ureidoglycine aminohydrolase
K: Ureidoglycine aminohydrolase
L: Ureidoglycine aminohydrolase
M: Ureidoglycine aminohydrolase
N: Ureidoglycine aminohydrolase
O: Ureidoglycine aminohydrolase
P: Ureidoglycine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,67948
Polymers483,67016
Non-polymers3,00932
Water10,773598
1
A: Ureidoglycine aminohydrolase
B: Ureidoglycine aminohydrolase
C: Ureidoglycine aminohydrolase
D: Ureidoglycine aminohydrolase
G: Ureidoglycine aminohydrolase
I: Ureidoglycine aminohydrolase
J: Ureidoglycine aminohydrolase
K: Ureidoglycine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,33924
Polymers241,8358
Non-polymers1,50416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26420 Å2
ΔGint-204 kcal/mol
Surface area69980 Å2
MethodPISA
2
E: Ureidoglycine aminohydrolase
F: Ureidoglycine aminohydrolase
H: Ureidoglycine aminohydrolase
L: Ureidoglycine aminohydrolase
M: Ureidoglycine aminohydrolase
N: Ureidoglycine aminohydrolase
O: Ureidoglycine aminohydrolase
P: Ureidoglycine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,33924
Polymers241,8358
Non-polymers1,50416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-201 kcal/mol
Surface area70190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.098, 174.894, 154.300
Angle α, β, γ (deg.)90.000, 99.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ureidoglycine aminohydrolase / (S)-Ureidoglycine Aminohydrolase


Mass: 30229.371 Da / Num. of mol.: 16 / Fragment: UNP residues 36-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ylbA, UGLYAH, At4g17050, AT4G17050 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GXV5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-UGY / (2S)-amino(carbamoylamino)ethanoic acid / (S)-2-ureidoglycine


Type: peptide linking / Mass: 133.106 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H7N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 8% (w/v) PEG 8000, 8% (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 140969

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.21refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.59→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2708 14114 9.3 %
Rwork0.2094 --
obs-140969 93.3 %
Solvent computationBsol: 32.3768 Å2
Displacement parametersBiso max: 73.52 Å2 / Biso mean: 40.5207 Å2 / Biso min: 4.05 Å2
Baniso -1Baniso -2Baniso -3
1-5.446 Å20 Å2-3.466 Å2
2---3.328 Å20 Å2
3----2.118 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33216 0 160 598 33974
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.9711.5
X-RAY DIFFRACTIONc_scbond_it1.3812
X-RAY DIFFRACTIONc_mcangle_it1.5952
X-RAY DIFFRACTIONc_scangle_it2.0322.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4UGY.param

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