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- PDB-5y3u: NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransfe... -

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Entry
Database: PDB / ID: 5y3u
TitleNMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV in the Presence of Polysialic Acid (PolySia)
ComponentsPSTD-22AA-PolySia
KeywordsTRANSFERASE / Polysialic Acid (PolySia) / Polysialyltransferase (polyST) / Polysialyltransferase Domain (PSTD)
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialyltransferase activity / sialylation / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / NCAM1 interactions ...Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialyltransferase activity / sialylation / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / NCAM1 interactions / protein glycosylation / protein modification process / nervous system development / Golgi membrane / Golgi apparatus / extracellular region
Similarity search - Function
Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase)
Similarity search - Domain/homology
CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiao, S.M. / Liu, X.H. / Lu, B. / Peng, L.X. / Chen, D. / Huang, R.B. / Zhou, G.P.
Funding support China, 5items
OrganizationGrant numberCountry
Guangxi science and technology cooperation program151707 China
The basic research program of Guangxi Academy of Sciences15YJ22SW02 China
The basic research program of Guangxi Academy of Sciences2017YJJ2 China
Guangxi science and technology cooperation program15104001-6 China
National Natural Science Foundation of China31560251 China
CitationJournal: To Be Published
Title: NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV in the Presence of Polysialic Acid (PolySia)
Authors: Lu, B. / Liao, S.M. / Lu, Z.L. / Liu, X.H. / Troy II, F.A. / Zhou, G.P. / Huang, R.B.
History
DepositionJul 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSTD-22AA-PolySia


Theoretical massNumber of molelcules
Total (without water)2,6241
Polymers2,6241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2610 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide PSTD-22AA-PolySia / CMP-N-acetylneuraminate-poly-alpha-2 / 8-sialyltransferase


Mass: 2624.181 Da / Num. of mol.: 1 / Fragment: UNP residues 258-279 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92187, EC: 2.4.99.-

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM PSTD-22AA-PolySia, 0.25 mM PolySia, 40 v/v ethyl group deuterated trifluoroethanol-d5, trifluoroethanol/water
Details: The compound of the 22 AA PSTD-pepptide and the clominic acid were dissolved in 40% (v/v) aqueous TFE-d2 (2,2,2-Trifluoroethanol-1,1-d2).
Label: sample1 / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPSTD-22AA-PolySianone1
0.25 mMPolySianone1
40 v/vtrifluoroethanol-d5ethyl group deuterated1
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AnalysisCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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