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- PDB-7p9l: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -

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Basic information

Entry
Database: PDB / ID: 7p9l
TitleN-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate
ComponentsUbiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
KeywordsSUGAR BINDING PROTEIN / N-acetylglucosamine recycling / carbohydrate kinase / ROK kinase.
Function / homology
Function and homology information


N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors ...N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / peptidoglycan turnover / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / PML body / protein tag activity / zinc ion binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
N-acetyl-D-glucosamine kinase / : / ROK family signature. / ROK family / ROK family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin domain profile. ...N-acetyl-D-glucosamine kinase / : / ROK family signature. / ROK family / ROK family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-4QY / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Ubiquitin-like protein SMT3 / N-acetyl-D-glucosamine kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Plesiomonas shigelloides 302-73 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRoy, S. / Isupov, M.N. / Harmer, N.J. / Ames, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N001591/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases
Authors: Cross, A.R. / Roy, S. / Vivoli Vega, M. / Rejzek, M. / Nepogodiev, S.A. / Cliff, M. / Salmon, D. / Isupov, M.N. / Field, R.A. / Prior, J.L. / Harmer, N.J.
History
DepositionJul 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
BBB: Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,31843
Polymers91,9202
Non-polymers3,39841
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-53 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.508, 114.508, 119.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 0 - 301 / Label seq-ID: 115 - 416

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein / Sugars , 2 types, 4 molecules AAABBB

#1: Protein Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase / GlcNAc kinase


Mass: 45960.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Plesiomonas shigelloides 302-73 (bacteria)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15, nagK, PLESHI_11010 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12306, UniProt: R8APY9, N-acetylglucosamine kinase
#4: Sugar ChemComp-4QY / 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose / beta-N-acetylglucosamine-6-phosphate / N-acetyl-6-O-phosphono-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 8 types, 392 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 90 mM halogens; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition B9 from Morpheus screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→99.17 Å / Num. obs: 90389 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / CC1/2: 0.998 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 4505 / CC1/2: 0.194

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DB3

4db3


Resolution: 1.75→76.252 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.904 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.1 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2226 4568 5.056 %
Rwork0.1929 85782 -
all0.194 --
obs-90350 99.02 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 36.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å2-0.006 Å2-0 Å2
2---0.012 Å2-0 Å2
3---0.038 Å2
Refinement stepCycle: LAST / Resolution: 1.75→76.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 200 353 5199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125221
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6517063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83721.341276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21415863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7861542
X-RAY DIFFRACTIONr_chiral_restr0.1120.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023929
X-RAY DIFFRACTIONr_nbd_refined0.2140.22525
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2340
X-RAY DIFFRACTIONr_metal_ion_refined0.3450.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.227
X-RAY DIFFRACTIONr_mcbond_it6.2536.3712521
X-RAY DIFFRACTIONr_mcangle_it7.29911.7753168
X-RAY DIFFRACTIONr_scbond_it8.0597.6382698
X-RAY DIFFRACTIONr_scangle_it10.11113.5273852
X-RAY DIFFRACTIONr_lrange_it11.61664.05122076
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.059718
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.092960.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.092960.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.3563250.33463750.33567010.6750.70299.98510.334
1.795-1.8450.3233170.31961840.31965050.7870.79499.93850.315
1.845-1.8980.313060.28960060.2963140.8250.84899.96830.281
1.898-1.9560.3122790.27258800.27461630.8540.87299.93510.258
1.956-2.0210.3093090.25956810.26160090.8620.88899.68380.243
2.021-2.0910.2642620.23754600.23957490.9070.91399.53030.221
2.091-2.170.253010.22152760.22356200.9220.93199.23490.202
2.17-2.2590.2352470.21250290.21353620.9370.9498.39610.192
2.259-2.3590.2252460.19648780.19751600.9410.9599.30230.173
2.359-2.4740.212280.18746750.18849290.9480.95499.47250.165
2.474-2.6080.2043000.16944220.17147300.9550.96499.83090.15
2.608-2.7660.2152160.17542040.17744300.9490.96299.77430.159
2.766-2.9570.2192180.18139960.18342280.9490.96299.66890.165
2.957-3.1930.2142280.18236730.18439240.9530.96199.41390.171
3.193-3.4970.2161850.17633750.17836110.9520.96698.58760.17
3.497-3.9090.2151690.16530220.16732810.9570.9797.25690.166
3.909-4.5120.1781420.15326520.15429150.9720.97595.84910.158
4.512-5.5210.1741440.15222140.15325130.9710.97593.83210.159
5.521-7.7870.206900.1817540.18119500.9560.96394.56410.185
7.787-76.2520.216560.18310240.18411470.9510.96294.15870.203

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