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- PDB-1pn3: Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in comp... -

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Basic information

Entry
Database: PDB / ID: 1pn3
TitleCrystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.
Components
  • DESVANCOSAMINYL VANCOMYCIN
  • GLYCOSYLTRANSFERASE GTFA
KeywordsTRANSFERASE/ANTIBIOTIC / GT-B GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / VANCOMYCIN / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


chloroorienticin B synthase / vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / : / carbohydrate metabolic process
Similarity search - Function
Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DESVANCOSAMINYL VANCOMYCIN / beta-D-glucopyranose / THYMIDINE-5'-DIPHOSPHATE / : / dTDP-epi-vancosaminyltransferase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsMulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / Walsh, C.T. / Garavito, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of the Tdp-Epi-Vancosaminyltransferase Gtfa from the Chloroeremomycin Biosynthetic Pathway.
Authors: Mulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / Walsh, C.T. / Garavito, R.M.
History
DepositionJun 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 2.0Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYLTRANSFERASE GTFA
B: GLYCOSYLTRANSFERASE GTFA
C: DESVANCOSAMINYL VANCOMYCIN
D: DESVANCOSAMINYL VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6097
Polymers87,8474
Non-polymers7633
Water2,918162
1
A: GLYCOSYLTRANSFERASE GTFA
C: DESVANCOSAMINYL VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5064
Polymers43,9232
Non-polymers5822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-19.9 kcal/mol
Surface area16000 Å2
MethodPISA
2
B: GLYCOSYLTRANSFERASE GTFA
D: DESVANCOSAMINYL VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1043
Polymers43,9232
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.8 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.500, 152.500, 98.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer.

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Components

#1: Protein GLYCOSYLTRANSFERASE GTFA


Mass: 42773.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Gene: GTFA / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96558
#2: Protein/peptide DESVANCOSAMINYL VANCOMYCIN


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4.
Source: (natural) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, DESVANCOSAMINYL VANCOMYCIN
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4.
References: DESVANCOSAMINYL VANCOMYCIN
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE ...VANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A D-GLUCOSE HERE, DESVANCOSAMINYL ANCOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE LIGAND (HET) BGC.
Has protein modificationY

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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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growpH: 6.1
Details: NA,K PHOSPHATE, PH 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.3 M / Common name: sodium potassium phosphate / Details: pH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 31308 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.081 / Net I/σ(I): 15.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6 % / Rsym value: 0.295 / % possible all: 99.8
Reflection
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Rmerge(I) obs: 0.295

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Processing

Software
NameVersionClassification
SOLVEV. 2.0phasing
RESOLVEV. 2.0model building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEV. 2.0phasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.249 1418 RANDOM
Rwork0.212 --
obs0.212 31308 -
Displacement parametersBiso mean: 44.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5797 0 47 162 6006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.97
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Rfactor all: 5 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.97
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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