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- PDB-1hxp: NUCLEOTIDE TRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1hxp
TitleNUCLEOTIDE TRANSFERASE
ComponentsHEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
KeywordsNUCLEOTIDYL TRANSFERASE / METALLOENZYME / GALACTOSEMIA / COMPLEX (SERINE PROTEASE-INHIBITOR)
Function / homology
Function and homology information


UDP-glucose-hexose-1-phosphate uridylyltransferase / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactokinase activity / galactose catabolic process via UDP-galactose / ferrous iron binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Galactose-1-phosphate uridyl transferase, class I His-active site / Galactose-1-phosphate uridyl transferase family 1 active site signature. / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily ...Galactose-1-phosphate uridyl transferase, class I His-active site / Galactose-1-phosphate uridyl transferase family 1 active site signature. / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / URIDINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Galactose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWedekind, J.E. / Frey, P.A. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1995
Title: Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 A resolution.
Authors: Wedekind, J.E. / Frey, P.A. / Rayment, I.
#1: Journal: Biochemistry / Year: 1995
Title: Galactose-1-Phosphate Uridylyltransferase from Escherichia Coli, a Zinc and Iron Metalloenzyme
Authors: Ruzicka, F.J. / Wedekind, J.E. / Kim, J. / Rayment, I. / Frey, P.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization and Preliminary Crystallographic Analysis of Galactose-1-Phosphate Uridylyltransferase from Escherichia Coli
Authors: Wedekind, J.E. / Frey, P.A. / Rayment, I.
History
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
B: HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,67512
Polymers79,3912
Non-polymers1,28310
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-64 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.600, 217.200, 69.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.94411, -0.01072, 0.32945), (-0.01135, -0.99994), (0.32943, -0.00374, -0.94417)
Vector: -10.37684, 159.46695, 66.34219)
DetailsTHE CRYSTALLOGRAPHICALLY INDEPENDENT UNIT IS ONE DIMER OF CHEMICALLY IDENTICAL SUBUNITS.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE / ALPHA-D-GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE


Mass: 39695.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE-UMP/UDP COMPLEX
Source: (gene. exp.) Escherichia coli (E. coli) / Description: PET VECTOR SYSTEM / Cell line: BL21 / Gene: GALT / Plasmid: PTZ18ROT / Gene (production host): GALT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) (PLYSS) / References: UniProt: P09148, EC: 2.7.7.10

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Non-polymers , 6 types, 479 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#6: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS ENTRY REPRESENTS THE STRUCTURE OF GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE COMPLEXED WITH UMP ...THIS ENTRY REPRESENTS THE STRUCTURE OF GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE COMPLEXED WITH UMP AND UDP. ATTENUATION OR DEFICIENCY OF THIS ENZYME RESULTS IN GALACTOSEMIA. THE PRESENT POSITION OF THE NUCLEOTIDE ALPHA PHOSPHORUS PRECLUDES THE ABILITY OF THE NUCLEOPHILE HIS 166 TO REACT. THIS INACTIVE CONFORMATION HAS BEEN ADOPTED DUE TO THE COVALENT MODIFICATION OF CYSTEINE 160 BY 2-MERCAPTOETHANOL. THE TURN CONTAINING CYS 52 AND CYS 55 OF THE ZINC BINDING MOTIF RESEMBLES THE RUBREDOXIN KNUCKLE.
Nonpolymer detailsTHE NUCLEOTIDE BINDS PERPENDICULARLY TO STRANDS B(ETA)-3, B(ETA)-6, B(ETA)-7 AND B(ETA)-8 OF THE ...THE NUCLEOTIDE BINDS PERPENDICULARLY TO STRANDS B(ETA)-3, B(ETA)-6, B(ETA)-7 AND B(ETA)-8 OF THE HALF-BARREL. THE IRON BINDING SITE HAS BEEN IDENTIFIED BY ITS ANOMALOUS DISPERSION SIGNAL. THE METAL COMPOSITION OF THIS ENZYME HAS BEEN REPORTED IN RUZICKA ET AL., 1995. MOST LIKELY THE IRON SITE CONTAINS A MIXTURE OF ZINC AND IRON. THERE IS NO CONFORMATIONAL DISORDER. THE OCCUPANCY OF IRON HAS BEEN MODELED AS UNITY AT THE FRN SITE. THE OXIDATION STATE OF THE ZINC OF (II) IS MOST LIKELY. THE IRON SITE IS LIKELY TO BE PREDOMINANTLY IN THE (III) STATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57 % / Description: NUMBER OF OBSERVED REFLECTIONS = 169713
Crystal grow
*PLUS
Temperature: 277 K / pH: 5.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117.5-23 mg/mlprotein1drop
214.5 %(v/v)PEG100001reservoir
3400 mM1reservoirLi2SO4
4250 mM1reservoirNaCl
54 mMphenyl-UDP1reservoir
61 mM1reservoirNaN3

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Data collection

DetectorDate: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 2 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 68553 / % possible obs: 82 % / Num. measured all: 169713 / Rmerge(I) obs: 0.022
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.94 Å / % possible obs: 70 % / Num. unique obs: 11827 / Num. measured obs: 31548 / Rmerge(I) obs: 0.096

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
XSCALIBREdata scaling
RefinementResolution: 1.8→50 Å / σ(F): 0
Details: DESPITE THE PRESENCE OF THE NUCLEOTIDE PHOSPHATE(S) THE LOOP REGION ADJACENT TO THE ACTIVE SITE FROM GLY 159 THROUGH ASN 162 EXHIBITS UNUSUALLY HIGH TEMPERATURE FACTORS.
RfactorNum. reflection
obs0.186 68553
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 66 469 5889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.254
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.006
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.2

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