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- PDB-2pa4: Crystal structure of UDP-glucose pyrophosphorylase from Corynebac... -

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Basic information

Entry
Database: PDB / ID: 2pa4
TitleCrystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose
ComponentsUTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
KeywordsTRANSFERASE / phosphorylase / nucleotidyltransferase / metabolism
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta / URIDINE-5'-DIPHOSPHATE-GLUCOSE / :
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: Protein Sci. / Year: 2007
Title: Active site geometry of glucose-1-phosphate uridylyltransferase.
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 8, 2013Group: Non-polymer description
Revision 1.4Feb 21, 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_auth_seq_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.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: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
B: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
C: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
D: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,58216
Polymers139,1234
Non-polymers2,46012
Water9,782543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
C: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7918
Polymers69,5612
Non-polymers1,2306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-87 kcal/mol
Surface area23950 Å2
MethodPISA, PQS
3
A: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
D: UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7918
Polymers69,5612
Non-polymers1,2306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-83 kcal/mol
Surface area23420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)173.400, 47.600, 161.500
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a homo-tetramer comprised of chains A, B, C, and D as deposited in the pdb entry

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Components

#1: Protein
UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE


Mass: 34780.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: ATCC-13032 / Gene: galU1 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q6M6R3, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23% PEG-3400, 200 mM MgCl2, 200 mM NaCl, 10 mM UDP-glucose, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99848 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2006 / Details: mirrors
RadiationMonochromator: Double-crystal monochromater Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99848 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 78712 / Num. obs: 78712 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 33.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5571 / Rsym value: 0.198 / % possible all: 83.9

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Processing

Software
NameClassification
HKL-3000data collection
PHASERphasing
TNTrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SIR / Resolution: 2→20 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 7841 -random
Rwork0.201 ---
all0.204 78303 --
obs0.204 78303 88.8 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8895 0 152 543 9590

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