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- PDB-5in3: Crystal structure of glucose-1-phosphate bound nucleotidylated hu... -

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Basic information

Entry
Database: PDB / ID: 5in3
TitleCrystal structure of glucose-1-phosphate bound nucleotidylated human galactose-1-phosphate uridylyltransferase
ComponentsGalactose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / GALT / UMP-GALT / glucose-1-phosphate / galactose-1-phosphate uridylyltransferase
Function / homology
Function and homology information


Defective GALT can cause GALCT / UDP-glucose-hexose-1-phosphate uridylyltransferase / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / Galactose catabolism / UDP-alpha-D-glucose metabolic process / galactose metabolic process / galactose catabolic process via UDP-galactose / Golgi apparatus / 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
1-O-phosphono-alpha-D-glucopyranose / 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE / Galactose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKopec, J. / McCorvie, T. / Tallant, C. / Velupillai, S. / Shrestha, L. / Fitzpatrick, F. / Patel, D. / Chalk, R. / Burgess-Brown, N. / von Delft, F. ...Kopec, J. / McCorvie, T. / Tallant, C. / Velupillai, S. / Shrestha, L. / Fitzpatrick, F. / Patel, D. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: Hum.Mol.Genet. / Year: 2016
Title: Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase.
Authors: McCorvie, T.J. / Kopec, J. / Pey, A.L. / Fitzpatrick, F. / Patel, D. / Chalk, R. / Shrestha, L. / Yue, W.W.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Galactose-1-phosphate uridylyltransferase
A: Galactose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,99536
Polymers91,9542
Non-polymers3,04134
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint23 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.760, 107.990, 126.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 29:41 or resseq 43:45 or (resid...
21(chain B and (resseq 29:41 or resseq 43:45 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISTRPTRP(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB29 - 4151 - 63
12LEULEUSERSER(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB43 - 4565 - 67
13ALAALAALAALA(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB4668
14ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
15ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
16ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
17ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
18ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
19ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
110ASPASPTYRTYR(chain A and (resseq 29:41 or resseq 43:45 or (resid...AB28 - 36650 - 388
21HISHISTRPTRP(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA29 - 4151 - 63
22LEULEUSERSER(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA43 - 4565 - 67
23ALAALAALAALA(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA4668
24ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388
25ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388
26ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388
27ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388
28ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388
29ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388
210ALAALATYRTYR(chain B and (resseq 29:41 or resseq 43:45 or (resid...BA22 - 36644 - 388

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Galactose-1-phosphate uridylyltransferase / Gal-1-P uridylyltransferase / UDP-glucose--hexose-1-phosphate uridylyltransferase


Mass: 45976.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mutation N314D - common polymorphysim / Source: (gene. exp.) Homo sapiens (human) / Gene: GALT / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07902, UDP-glucose-hexose-1-phosphate uridylyltransferase
#5: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 456 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-H2U / 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 326.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O9P
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.8 Å3/Da / Density % sol: 56.06 % / Description: plate
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium sulfate -- 30%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→59.8 Å / Num. obs: 86007 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 0.996 / Net I/σ(I): 1
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4211 / CC1/2: 0.654 / % possible all: 62.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hxq

1hxq


Resolution: 1.73→40.29 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2278 4228 4.92 %
Rwork0.1983 --
obs0.1998 86007 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.08 Å2 / Biso mean: 38.7901 Å2 / Biso min: 15.29 Å2
Refinement stepCycle: final / Resolution: 1.73→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5300 0 398 424 6122
Biso mean--57.95 42.78 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095697
X-RAY DIFFRACTIONf_angle_d1.0627745
X-RAY DIFFRACTIONf_chiral_restr0.059803
X-RAY DIFFRACTIONf_plane_restr0.0081002
X-RAY DIFFRACTIONf_dihedral_angle_d12.5593356
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3885X-RAY DIFFRACTION6.899TORSIONAL
12B3885X-RAY DIFFRACTION6.899TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.74970.2281450.1982722X-RAY DIFFRACTION100
1.8902-1.91840.29761330.28642690X-RAY DIFFRACTION100
1.9184-1.94840.321410.29522694X-RAY DIFFRACTION100
1.9484-1.98030.32791190.27142695X-RAY DIFFRACTION100
1.9803-2.01450.30871290.25522701X-RAY DIFFRACTION100
2.0145-2.05110.30041700.25592711X-RAY DIFFRACTION100
2.0511-2.09060.27541320.26012682X-RAY DIFFRACTION100
2.0906-2.13320.31971380.25332728X-RAY DIFFRACTION100
2.1332-2.17960.29351290.24812708X-RAY DIFFRACTION100
2.1796-2.23030.27251180.2382711X-RAY DIFFRACTION100
2.2303-2.28610.28191530.21122719X-RAY DIFFRACTION100
2.2861-2.34790.271480.21322698X-RAY DIFFRACTION100
2.3479-2.4170.22071280.19662731X-RAY DIFFRACTION100
2.417-2.4950.25751600.19742706X-RAY DIFFRACTION100
2.495-2.58410.24821500.19792715X-RAY DIFFRACTION100
2.5841-2.68760.20731370.1872739X-RAY DIFFRACTION100
2.6876-2.80990.21381460.17982724X-RAY DIFFRACTION100
2.8099-2.9580.21221180.18112763X-RAY DIFFRACTION100
2.958-3.14320.20821420.18622760X-RAY DIFFRACTION100
3.1432-3.38580.18921450.17012750X-RAY DIFFRACTION100
3.3858-3.72630.20551400.16592782X-RAY DIFFRACTION100
3.7263-4.2650.15671660.14242758X-RAY DIFFRACTION100
4.265-5.37140.14331250.1332845X-RAY DIFFRACTION100
5.3714-40.290.18521620.17272935X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.848 Å / Origin y: -6.4725 Å / Origin z: 10.1401 Å
111213212223313233
T0.1629 Å2-0.018 Å20.0129 Å2-0.1592 Å2-0.0083 Å2--0.1884 Å2
L0.5103 °20.0041 °20.2354 °2-0.6602 °2-0.1295 °2--1.4093 °2
S-0.0354 Å °0.0689 Å °0.0306 Å °-0.0215 Å °0.0135 Å °0.0362 Å °-0.0707 Å °0.0784 Å °0.0236 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB22 - 366
2X-RAY DIFFRACTION1allA28 - 366
3X-RAY DIFFRACTION1allF2 - 3
4X-RAY DIFFRACTION1allC2
5X-RAY DIFFRACTION1allC3
6X-RAY DIFFRACTION1allE1 - 28
7X-RAY DIFFRACTION1allE29
8X-RAY DIFFRACTION1allE30 - 31
9X-RAY DIFFRACTION1allH1 - 2
10X-RAY DIFFRACTION1allS1 - 460

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