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- PDB-7p9p: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -

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Basic information

Entry
Database: PDB / ID: 7p9p
TitleN-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and AMP-PNP inhibitor
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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation ...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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / peptidoglycan turnover / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / 2-acetamido-2-deoxy-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 2.11 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)95,26532
Polymers91,9202
Non-polymers3,34430
Water4,630257
1
BBB: Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)95,26532
Polymers91,9202
Non-polymers3,34430
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,x-1,-z1
Buried area9270 Å2
ΔGint-42 kcal/mol
Surface area25420 Å2
Unit cell
Length a, b, c (Å)115.202, 115.202, 120.360
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: -1 - 301 / Label seq-ID: 114 - 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
#6: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 285 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 60 mM divalent cations; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K. Condition A3 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.11→57.6 Å / Num. obs: 53533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 10 % / CC1/2: 0.998 / Net I/σ(I): 9.5
Reflection shellResolution: 2.11→2.17 Å / Num. unique obs: 4354 / CC1/2: 0.336

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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: 2.11→29.107 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.231 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.161 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.233 2794 5.225 %
Rwork0.1914 50678 -
all0.194 --
obs-53472 99.935 %
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: 50.004 Å2
Baniso -1Baniso -2Baniso -3
1--1.845 Å2-0.923 Å2-0 Å2
2---1.845 Å2-0 Å2
3---5.986 Å2
Refinement stepCycle: LAST / Resolution: 2.11→29.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 199 257 5106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125079
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6496860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61121.609261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60215799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711536
X-RAY DIFFRACTIONr_chiral_restr0.1060.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023818
X-RAY DIFFRACTIONr_nbd_refined0.2170.22393
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2266
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.215
X-RAY DIFFRACTIONr_mcbond_it6.8029.2552467
X-RAY DIFFRACTIONr_mcangle_it8.21217.1863088
X-RAY DIFFRACTIONr_scbond_it9.26310.3932612
X-RAY DIFFRACTIONr_scangle_it11.50518.7713760
X-RAY DIFFRACTIONr_lrange_it12.78491.57221296
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.059418
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.08880.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.08880.05009
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
2.11-2.1650.412090.37736720.37938820.610.64199.97420.381
2.165-2.2240.3591740.35436280.35538030.6820.67799.97370.355
2.224-2.2880.3421780.32734930.32836710.7220.7211000.321
2.288-2.3580.331800.30434430.30536230.7670.7841000.29
2.358-2.4340.3131780.29332850.29434630.8280.8161000.276
2.434-2.5190.3181500.26832330.2733830.8470.8621000.246
2.519-2.6140.2652110.24830490.24932600.8960.8991000.224
2.614-2.7190.251650.21829650.2231320.9120.92399.93610.191
2.719-2.8390.2581690.21728470.21930160.9040.931000.187
2.839-2.9760.2471340.17727790.1829130.9340.9541000.15
2.976-3.1360.241470.18425950.18727430.9450.95499.96350.157
3.136-3.3230.2211590.17324610.17626200.9450.961000.147
3.323-3.5490.2341270.1723280.17324550.9430.9651000.15
3.549-3.8290.1961360.15921680.16223050.9640.97299.95660.143
3.829-4.1870.184810.14820370.14921180.9680.9751000.134
4.187-4.670.1511060.1318380.13119440.9790.9821000.121
4.67-5.3690.178950.13816350.1417300.9720.9771000.126
5.369-6.520.226960.17413900.17814860.9540.9661000.16
6.52-8.9980.254620.16911230.17311850.9410.971000.157
8.998-29.1070.225370.1657090.1687480.9560.97299.73260.162

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