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- PDB-2ch6: Crystal structure of human N-acetylglucosamine kinase in complex ... -

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Basic information

Entry
Database: PDB / ID: 2ch6
TitleCrystal structure of human N-acetylglucosamine kinase in complex with ADP and glucose
ComponentsN-ACETYL-D-GLUCOSAMINE KINASE
KeywordsTRANSFERASE / SUGAR KINASE / RIBONUCLEASE H FOLD / SUGAR KINASE/HSP70/ACTIN SUPERFAMILY
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 / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / N-acetylglucosamine metabolic process ...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 / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / N-acetylglucosamine metabolic process / 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
ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / N-acetyl-D-glucosamine kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 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: Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / software / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYL-D-GLUCOSAMINE KINASE
B: N-ACETYL-D-GLUCOSAMINE KINASE
C: N-ACETYL-D-GLUCOSAMINE KINASE
D: N-ACETYL-D-GLUCOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,10012
Polymers149,6704
Non-polymers2,4298
Water00
1
A: N-ACETYL-D-GLUCOSAMINE KINASE
D: N-ACETYL-D-GLUCOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0506
Polymers74,8352
Non-polymers1,2154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-24.7 kcal/mol
Surface area29710 Å2
MethodPISA
2
B: N-ACETYL-D-GLUCOSAMINE KINASE
C: N-ACETYL-D-GLUCOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0506
Polymers74,8352
Non-polymers1,2154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-25.7 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.710, 101.992, 110.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96727, -0.18627, -0.17233), (0.2353, -0.91261, -0.33432), (-0.095, -0.36393, 0.92657)154.22133, 128.66124, -33.4981
2given(-0.78777, 0.46701, -0.40165), (-0.60797, -0.48475, 0.6288), (0.09895, 0.73954, 0.6658)68.0626, 60.03337, -48.91132
3given(-0.9293, -0.34685, 0.12688), (-0.34543, 0.69471, -0.63092), (0.13068, -0.63014, -0.7654)144.12819, 89.39929, 162.9726
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO NAGK DIMERS (CHAINS AD FORM ONE, AND CHAINS C AND B FORM THE OTHER).

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Components

#1: Protein
N-ACETYL-D-GLUCOSAMINE KINASE / N-ACETYLGLUCOSAMINE KINASE / NAGK PROTEIN / PROTEIN TMP_LOCUS_2 / GLCNAC KINASE


Mass: 37417.609 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: Q9UJ70, N-acetylglucosamine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.6 Å3/Da / Density % sol: 51.9 %
Description: MAD DATA OF SEMET LABELED CRYSTALS WERE COLLECTED AT PROTEIN STRUCTURE FACTORY BEAMLINE BL2 OF FREE UNIVERSITY BERLIN AT BESSY
Crystal growpH: 5.6
Details: 100 MM MES PH5.6, 100 MM NACL, 2% (W/V) PEG 20K, pH 5.60

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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: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.72→30 Å / Num. obs: 40858 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 2.72→2.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 2.72→29.8 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / SU B: 27.79 / SU ML: 0.32 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2093 5.1 %RANDOM
Rwork0.227 ---
obs0.231 39284 100 %-
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: 53.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2--2.77 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.72→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10159 0 156 0 10315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9814255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54451322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16623.178450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.843151699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0891574
X-RAY DIFFRACTIONr_chiral_restr0.0970.21556
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.24525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27096
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.2163
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4991.56712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.884210380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14634363
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.854.53875
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: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 161 -
Rwork0.3 2824 -
obs--100 %
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)
11.8193-0.9054-0.59494.8985-0.26882.28040.1787-0.1090.2859-0.0371-0.0518-0.2583-0.2158-0.0243-0.1268-0.2909-0.02390.0367-0.32110.0251-0.110135.04794.34574.0381
21.71360.8461-0.27723.5827-1.90073.17290.1919-0.707-0.6430.7613-0.3027-0.21830.2628-0.25270.11080.2913-0.1224-0.08540.3930.1797-0.019315.682560.8839115.2026
34.1743-2.3728-0.41835.24550.26362.38780.03390.8609-0.6549-0.5973-0.2481-0.09290.74640.4760.21420.1106-0.00480.03160.31210.0016-0.041797.846414.7428132.0132
41.9865-0.6426-0.15446.8708-2.75972.67790.0934-0.06390.1411-0.32830.10530.536-0.14950.0751-0.1987-0.1366-0.0157-0.0839-0.1667-0.09770.014689.113797.5949.4314
52.83010.2377-1.42331.57450.73882.9101-0.1245-0.1446-0.12180.12370.0103-0.00170.31850.12630.1142-0.18360.0613-0.0776-0.28230.0134-0.215553.089375.357867.1176
65.84331.64211.95512.18590.84653.51040.2322-0.5362-0.9272-0.0297-0.0727-0.43030.08470.0629-0.1595-0.14340.06520.0108-0.14130.1504-0.04114.138771.06993.3072
73.2665-0.1271.45561.36330.00943.3798-0.10840.67920.1848-0.1378-0.1258-0.0942-0.21120.19040.2342-0.0953-0.08180.0044-0.02650.0988-0.182575.71330.7812128.5244
85.2709-0.4112-1.89421.5860.36133.3683-0.0441-0.85890.20410.08250.0814-0.1041-0.11350.4415-0.0373-0.16720.0419-0.0934-0.1245-0.0603-0.212776.188781.979371.8776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 119
2X-RAY DIFFRACTION1A334 - 344
3X-RAY DIFFRACTION2B3 - 119
4X-RAY DIFFRACTION2B334 - 344
5X-RAY DIFFRACTION3C3 - 119
6X-RAY DIFFRACTION3C334 - 344
7X-RAY DIFFRACTION4D3 - 119
8X-RAY DIFFRACTION4D334 - 344
9X-RAY DIFFRACTION5A120 - 291
10X-RAY DIFFRACTION6B120 - 291
11X-RAY DIFFRACTION7C120 - 291
12X-RAY DIFFRACTION8D120 - 291

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