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- PDB-1hxq: THE STRUCTURE OF NUCLEOTIDYLATED GALACTOSE-1-PHOSPHATE URIDYLYLTR... -

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Basic information

Entry
Database: PDB / ID: 1hxq
TitleTHE STRUCTURE OF NUCLEOTIDYLATED GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE FROM ESCHERICHIA COLI AT 1.86 ANGSTROMS RESOLUTION
ComponentsHEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
KeywordsNUCLEOTIDYLTRANSFERASE / METALLOENZYME / NUCLEOTIDYLATED HISTIDINE / REACTION INTERMEDIATE
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, Leloir pathway / ferrous iron binding / zinc ion binding / cytosol / cytoplasm
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
: / URIDINE-5'-MONOPHOSPHATE / Galactose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.86 Å
AuthorsWedekind, J.E. / Frey, P.A. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1996
Title: The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer.
Authors: Wedekind, J.E. / Frey, P.A. / Rayment, I.
#1: 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.
#2: 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.
#3: 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.
#4: Journal: Nucleic Acids Res. / Year: 1987
Title: The Nucleotide Sequence of the Gal T Gene of Escherichia Coli
Authors: Cornwell, T.L. / Adhya, S.L. / Reznikoff, W.S. / Frey, P.A.
History
DepositionJun 16, 1996Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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
Revision 1.4Oct 16, 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_conn_type / struct_site
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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

Downloads & links

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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)80,2808
Polymers79,3892
Non-polymers8916
Water13,151730
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-67 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 215.400, 68.900
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: (0.94373, -0.00281, 0.33071), (-0.00297, -1, -2.0E-5), (0.33071, -0.00096, -0.94373)
Vector: -10.90264, 158.00136, 65.75232)
DetailsTHE CRYSTALLOGRAPHICALLY INDEPENDENT UNIT IS ONE DIMER OF CHEMICALLY IDENTICAL SUBUNITS.

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Components

#1: Protein HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE / ALPHA-D-GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE / GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE- ...ALPHA-D-GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE / GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE-URIDYLYLATED HIS 166


Mass: 39694.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 / Plasmid: PTZ18ROT / Gene (production host): GALT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS
References: UniProt: P09148, UDP-glucose-hexose-1-phosphate uridylyltransferase
#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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGLN 168 MAKES CLOSE CONTACTS TO O2 OF THE U5P PHOSPHORYL GROUP. MUTATION OF THIS RESIDUE TO ARG HAS ...GLN 168 MAKES CLOSE CONTACTS TO O2 OF THE U5P PHOSPHORYL GROUP. MUTATION OF THIS RESIDUE TO ARG HAS BEEN INVOKED AS A PREDOMINANT CAUSE OF THE HUMAN METABOLIC DISEASE GALACTOSEMIA. GLN 168 MAY PLAY A ROLE IN BINDING THE BETA-PHOSPHORYL GROUP OF THE HEXOSE-1-PHOSPHATE SUBSTRATE AS WELL.
Has protein modificationY
Nonpolymer detailsTHIS ENTRY REPRESENTS THE STRUCTURE OF GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE IN WHICH NE2 OF ...THIS ENTRY REPRESENTS THE STRUCTURE OF GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE IN WHICH NE2 OF HIS-166 IS COVALENTLY LINKED AS A PHOSPHORAMIDATE TO THE ALPHA-PHOSPHORUS OF U5P. THIS IS A GENUINE REACTION INTERMEDIATE IN THE NET DOUBLE DISPLACEMENT REACTION. THE REACTION PROCEEDS WITH TWO DISPLACEMENTS AS FOLLOWS: UDP-GLC + ENZYME-HIS 166 <--> GLC-1-P + ENZYME-HIS 166-U5P ENZYME-HIS 166-U5P + GAL-1-P <--> UDP-GAL + ENZYME-HIS 166. THE NUCLEOTIDE IS BOUND PERPENDICULARLY TO STRANDS B(ETA) -3, B(ETA)-6, B(ETA)-7 AND B(ETA)-8 OF THE HALF-BARREL. THE METAL COMPOSITION OF THIS ENZYME HAS BEEN REPORTED BY 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 SET TO UNITY. THE OXIDATION STATE OF THE ZINC IS (II) 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 / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growpH: 7.1
Details: EACH CRYSTAL WAS REACTED WITH SUBSTRATE UDP-GLUCOSE IN A SYNTHETIC MOTHER LIQUOR DEVOID OF LITHIUM SULFATE AT PH 7.1.
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 %(w/v)PEG100001reservoir
20.40 M1reservoirLi2SO4
30.25 M1reservoirNaCl
40.10 Msodium succinate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: 1995 / Details: SUPPER DOUBLE-FOCUSING MIRRORS WITH NICKEL FOIL
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→65 Å / Num. obs: 70581 / % possible obs: 97 % / Observed criterion σ(I): -1 / Redundancy: 2.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.063
Reflection
*PLUS
Num. all: 15045 / Num. measured all: 206202 / Rmerge(I) obs: 0.0625
Reflection shell
*PLUS
Highest resolution: 1.86 Å / % possible obs: 90 % / Num. unique obs: 10989 / Num. measured obs: 19085 / Rmerge(I) obs: 0.165

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Processing

Software
NameVersionClassification
TNT5Erefinement
SAINTdata reduction
XSCALIBREdata reduction
RefinementResolution: 1.86→65 Å / σ(F): 0
Details: REGIONS A 36 THROUGH A 44 AND B 31 THROUGH B 43 ARE DISORDERED. NO SIGNIFICANT ELECTRON DENSITY CAN BE SEEN FOR THESE REGIONS AT THE RESOLUTION OF THE REFINED MODEL. RESIDUES B 347 AND B 348 ...Details: REGIONS A 36 THROUGH A 44 AND B 31 THROUGH B 43 ARE DISORDERED. NO SIGNIFICANT ELECTRON DENSITY CAN BE SEEN FOR THESE REGIONS AT THE RESOLUTION OF THE REFINED MODEL. RESIDUES B 347 AND B 348 OF SUBUNIT II ARE DISORDERED AS WELL.
RfactorNum. reflection% reflection
Rwork0.196 --
all-70581 -
obs-206202 97 %
Solvent computationSolvent model: TNT / Bsol: 526 Å2 / ksol: 0.7 e/Å3
Refinement stepCycle: LAST / Resolution: 1.86→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5405 0 44 730 6179
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01356147
X-RAY DIFFRACTIONt_angle_deg2.14676674
X-RAY DIFFRACTIONt_dihedral_angle_d16.18629250
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle28.968491
X-RAY DIFFRACTIONt_trig_c_planes0.00314440
X-RAY DIFFRACTIONt_gen_planes0.005816120
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5-E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.00340
X-RAY DIFFRACTIONt_plane_restr0.005120

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