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- PDB-2ch5: Crystal structure of human N-acetylglucosamine kinase in complex ... -

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Basic information

Entry
Database: PDB / ID: 2ch5
TitleCrystal structure of human N-acetylglucosamine kinase in complex with N-acetylglucosamine
ComponentsNAGK PROTEIN
KeywordsTRANSFERASE / N-ACETYLGLUCOSAMINE / GLCNAC / SUGAR KINASE / RIBONUCLEASE H FOLD / SUGAR KINASE/HSP70/ACTIN SUPERFAMILY / DOMAIN ROTATION / OPEN CONFORMATION / CLOSED CONFORMATION / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


muramyl dipeptide kinase activity / N-acetylmannosamine metabolic process / N-acetylglucosamine kinase / N-acylmannosamine kinase / N-acetylglucosamine kinase activity / N-acylmannosamine kinase activity / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine catabolic process / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor ...muramyl dipeptide kinase activity / N-acetylmannosamine metabolic process / N-acetylglucosamine kinase / N-acylmannosamine kinase / N-acetylglucosamine kinase activity / N-acylmannosamine kinase activity / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine catabolic process / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / N-acetylneuraminate catabolic process / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / UDP-N-acetylglucosamine biosynthetic process / response to muramyl dipeptide / defense response to bacterium / innate immune response / extracellular exosome / ATP binding / cytosol
Similarity search - Function
N-acetyl-D-glucosamine kinase NAGK-like / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-D-glucosamine kinase / N-acetyl-D-glucosamine kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWeihofen, W.A. / Berger, M. / Chen, H. / Saenger, W. / Hinderlich, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structures of Human N-Acetylglucosamine Kinase in Two Complexes with N-Acetylglucosamine and with Adp/Glucose: Insights Into Substrate Specificity and Regulation.
Authors: Weihofen, W.A. / Berger, M. / Chen, H. / Saenger, W. / Hinderlich, S.
History
DepositionMar 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAGK PROTEIN
B: NAGK PROTEIN
C: NAGK PROTEIN
D: NAGK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,50513
Polymers151,1604
Non-polymers1,3459
Water22,9151272
1
A: NAGK PROTEIN
B: NAGK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2076
Polymers75,5802
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-12.5 kcal/mol
Surface area28100 Å2
MethodPISA
2
C: NAGK PROTEIN
D: NAGK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2997
Polymers75,5802
Non-polymers7195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-10.7 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.537, 98.482, 101.981
Angle α, β, γ (deg.)63.43, 75.66, 75.06
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99999, 0.00436, 0.0007), (0.00254, 0.43832, 0.89882), (0.00362, 0.89881, -0.43833)104.64798, -14.31278, 22.33683
2given(-1, 0.00098, 0.00078), (-0.00114, -0.46022, -0.88781), (-0.00051, -0.88781, 0.46022)101.34024, 253.64937, 150.31953
3given(0.99998, -0.00537, -0.00375), (-0.00527, -0.99965, 0.02596), (-0.00389, -0.02594, -0.99966)4.65503, 232.13608, 184.94237

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Components

#1: Protein
NAGK PROTEIN / HUMAN N-ACETYLGLUCOSAMINE KINASE / PROTEIN TMP_LOCUS_2 / GLCNAC KINASE


Mass: 37790.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: CDNA FROM THE RESOURCE CENTER OF THE GERMAN HUMAN GENOME PROJECT
Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6IA84, UniProt: Q9UJ70*PLUS, N-acetylglucosamine kinase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1272 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLONING ARTEFACTS (3 RESIDUES) LINKED TO CHAINS A, B, C, D.

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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: 3.3 Å3/Da / Density % sol: 62.8 %
Crystal growpH: 5.6
Details: 100 MM HEPES PH 7.0, 100 MM NACL, 8% (W/V) PEG 4000, 2MM GLCNAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→2.05 Å / Num. obs: 140534 / % possible obs: 93.3 % / Observed criterion σ(I): 2.5 / Redundancy: 1.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN N-ACETYLGLUCOSAMINE KINASE IN COMPLEX WITH ADP AND GLUCOSE

Resolution: 1.9→90.17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.135 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 292 TO 294 OF CHAIN A, 294 TO 298 OF CHAIN B, 293 TO 297 OF CHAIN C, AND 294 TO 298 OF CHAIN D ARE PARTIALLY DISORDERED AND WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 292 TO 294 OF CHAIN A, 294 TO 298 OF CHAIN B, 293 TO 297 OF CHAIN C, AND 294 TO 298 OF CHAIN D ARE PARTIALLY DISORDERED AND WERE NOT MODELED DUE TO LACK OF ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2817 2 %RANDOM
Rwork0.167 ---
obs0.167 137744 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.04 Å2-1.37 Å2
2---0.18 Å20.83 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→90.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10482 0 89 1272 11843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210792
X-RAY DIFFRACTIONr_bond_other_d0.0020.029895
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.96914565
X-RAY DIFFRACTIONr_angle_other_deg0.833.00122857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03251358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88923.132463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.438151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6881576
X-RAY DIFFRACTIONr_chiral_restr0.1560.21588
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022284
X-RAY DIFFRACTIONr_nbd_refined0.2280.22227
X-RAY DIFFRACTIONr_nbd_other0.1910.29793
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25268
X-RAY DIFFRACTIONr_nbtor_other0.0870.25909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2867
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.2143
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0811.58712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.291210687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27734740
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2284.53878
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 186
Rwork0.232 8615
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4950.0865-0.20862.0946-0.16671.2875-0.02-0.0462-0.2882-0.0696-0.0193-0.0161-0.0917-0.03760.0393-0.12710.0029-0.022-0.08460.01150.033243.10972.4787.695
21.14770.2951-0.38041.3084-0.57681.25150.0678-0.14730.05370.3364-0.0834-0.1241-0.17780.0350.01560.0625-0.0135-0.0766-0.1168-0.0277-0.072754.8897.4991.116
33.48782.82080.13583.2395-0.16920.08650.1175-0.4424-0.11860.5369-0.16460.1462-0.2689-0.20370.04720.0169-0.0093-0.0329-0.03280.0281-0.028239.83976.769101.958
41.36310.2254-0.241.40970.34311.6924-0.02570.2936-0.03650.07540.0539-0.08130.08720.0318-0.0282-0.1301-0.0022-0.02460.0403-0.0019-0.066461.97796.51349.284
51.33470.0672-0.28851.0944-0.2991.54730.01120.0650.22220.05750.0031-0.0364-0.1887-0.0556-0.0143-0.02330.0195-0.0495-0.1254-0.0171-0.035150.253110.54570.312
63.9156-2.3215-2.05142.61041.80562.21580.13410.48330.3046-0.1251-0.0596-0.1306-0.3787-0.0206-0.0745-0.0444-0.0008-0.00970.03480.061-0.029865.295111.21746.884
71.4731-0.34260.26711.3205-0.02722.13780.0241-0.19690.1474-0.0776-0.0255-0.01590.0269-0.00570.0014-0.1231-0.0357-0.00970.0336-0.0191-0.072558.475138.891132.056
81.0993-0.1640.54730.7818-0.47721.93330.1178-0.0424-0.0662-0.0498-0.0174-0.0060.4435-0.1412-0.10040.0833-0.0649-0.032-0.0914-0.0083-0.105946.513124.551111.417
92.93061.83832.0461.16411.39942.65610.1677-0.202-0.2231-0.0175-0.0982-0.22640.55950.0543-0.06950.0273-0.0337-0.04090.02380.0058-0.07361.674124.317134.693
101.1372-0.00860.42622.0338-0.06371.20040.0074-0.01660.19980.1111-0.03310.0380.0325-0.03860.0258-0.13950.00470.0113-0.08120.02080.026639.691161.94692.9
110.8772-0.25810.45591.0101-0.30021.40630.07180.0531-0.0034-0.1234-0.0716-0.06630.13410.0579-0.0002-0.00540.00530.0046-0.07070.0098-0.041751.359136.77990.174
122.9079-2.8769-1.09114.07281.40790.89680.12140.28950.1437-0.3782-0.12110.10630.1225-0.2094-0.0003-0.02290.0157-0.0038-0.04370.05080.027736.397157.30378.767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 125
2X-RAY DIFFRACTION2A126 - 297
3X-RAY DIFFRACTION2A341 - 344
4X-RAY DIFFRACTION3A312 - 340
5X-RAY DIFFRACTION4B2 - 125
6X-RAY DIFFRACTION5B126 - 293
7X-RAY DIFFRACTION5B341 - 344
8X-RAY DIFFRACTION6B312 - 340
9X-RAY DIFFRACTION7C2 - 125
10X-RAY DIFFRACTION8C126 - 292
11X-RAY DIFFRACTION8C341 - 344
12X-RAY DIFFRACTION9C312 - 340
13X-RAY DIFFRACTION10D2 - 125
14X-RAY DIFFRACTION11D126 - 293
15X-RAY DIFFRACTION11D341 - 344
16X-RAY DIFFRACTION12D312 - 340

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