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- PDB-7pa1: Structure of N-acetylglucosamine kinase from Plesiomonas shigello... -

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Basic information

Entry
Database: PDB / ID: 7pa1
TitleStructure of N-acetylglucosamine kinase from Plesiomonas shigelloides in complex with AMP-PNP in the absence of N-acetylglucoseamine substrate
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 / 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: 2.2 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 28, 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)94,43521
Polymers91,9202
Non-polymers2,51519
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint6 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.265, 121.265, 91.684
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
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: LEU / End label comp-ID: LEU / Auth seq-ID: -1 - 302 / Label seq-ID: 114 - 417

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 , 1 types, 2 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

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Non-polymers , 6 types, 171 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.09M NPS; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition C9 from Morpheus crystallisation 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: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→60.63 Å / Num. obs: 38637 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.964 / Net I/σ(I): 5.2
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 3361 / CC1/2: 0.396

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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: 2.2→39.693 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.534 / SU ML: 0.234 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.208 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2517 1846 4.779 %
Rwork0.2076 36784 -
all0.21 --
obs-38630 99.168 %
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: 47.045 Å2
Baniso -1Baniso -2Baniso -3
1-0.417 Å20.209 Å20 Å2
2--0.417 Å20 Å2
3----1.353 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 154 152 4936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124915
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6426635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65322.129249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30615784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4841532
X-RAY DIFFRACTIONr_chiral_restr0.1190.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023710
X-RAY DIFFRACTIONr_nbd_refined0.2050.22252
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.23
X-RAY DIFFRACTIONr_mcbond_it6.4598.5452442
X-RAY DIFFRACTIONr_mcangle_it7.46915.9823052
X-RAY DIFFRACTIONr_scbond_it10.4549.9832473
X-RAY DIFFRACTIONr_scangle_it12.61918.0573577
X-RAY DIFFRACTIONr_lrange_it13.40587.29120457
X-RAY DIFFRACTIONr_ncsr_local_group_10.0780.059536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.078230.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.078230.05009
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
2.2-2.2570.4581250.41227230.41428550.4180.53899.75480.411
2.257-2.3190.3651480.36126160.36227710.5570.55799.74740.36
2.319-2.3860.3941450.34325650.34527340.6870.72699.12220.344
2.386-2.4590.3251230.33324910.33326260.7680.74799.5430.332
2.459-2.5390.3751050.33824270.3425370.7480.76999.80290.339
2.539-2.6280.3341060.30923680.3124870.8220.8299.47730.303
2.628-2.7270.3561190.30222460.30523730.8270.84299.66290.294
2.727-2.8370.319710.26822410.26923200.8690.8899.65520.249
2.837-2.9630.3361290.25920600.26422040.8840.90199.31940.236
2.963-3.1070.328890.22620080.2321060.8880.92399.57260.2
3.107-3.2730.2621180.2118880.21320260.9180.93499.01280.186
3.273-3.4710.27790.19617770.19918810.9270.94698.67090.174
3.471-3.7080.251120.18216640.18618090.9440.9698.17580.162
3.708-4.0020.2840.15815540.1616600.9580.96998.67470.144
4.002-4.380.191600.13814660.1415440.9630.97698.83420.131
4.38-4.890.152710.11513160.11714040.9790.98398.78920.111
4.89-5.6320.169570.11911680.12112410.9730.97998.71070.113
5.632-6.8630.174370.149840.14110450.9650.97597.70330.135
6.863-9.5640.149440.1527690.1518330.9680.97497.5990.156
9.564-39.6930.187240.1494520.1514900.8480.97397.14290.17

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