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- PDB-2yhw: High-resolution crystal structures of N-Acetylmannosamine kinase:... -

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Basic information

Entry
Database: PDB / ID: 2yhw
TitleHigh-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.
ComponentsBIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE
KeywordsTRANSFERASE / SIALIC ACID / MANNAC / ROK FAMILY
Function / homology
Function and homology information


Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism ...Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism / hydrolase activity, hydrolyzing O-glycosyl compounds / ATP binding / metal ion binding / cytosol
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase,UDP-hydrolysing / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-acetamido-2-deoxy-alpha-D-mannopyranose / TRIETHYLENE GLYCOL / Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.64 Å
AuthorsMartinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Zimmer, R. / Tauberger, E. / Reutter, W. / Saenger, W. / Fan, H. / Moniot, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition
Authors: Martinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Reutter, W. / Fan, H. / Saenger, W. / Moniot, S.
History
DepositionMay 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,00413
Polymers36,6201
Non-polymers1,38412
Water4,594255
1
A: BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE
hetero molecules

A: BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,00926
Polymers73,2402
Non-polymers2,76924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8040 Å2
ΔGint-31.3 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.730, 90.730, 100.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE / N-ACETYL MANNOSAMINE KINASE / MANAC KINASE / UDP-GLCNAC-2-EPIMERASE/MANAC KINASE


Mass: 36620.016 Da / Num. of mol.: 1
Fragment: N-ACETYLMANNOSAMINE KINASE DOMAIN, RESIDUES 406-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-MNK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9Y223, N-acylmannosamine kinase
#2: Sugar ChemComp-BM3 / 2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetyl-alpha-D-mannosamine / 2-acetamido-2-deoxy-alpha-D-mannose / 2-acetamido-2-deoxy-D-mannose / 2-acetamido-2-deoxy-mannose / 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DManpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 266 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 % / Description: NONE
Crystal growDetails: 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 40% PEG 300.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.64→45.3 Å / Num. obs: 52083 / % possible obs: 100 % / Observed criterion σ(I): 4.37 / Redundancy: 12.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.66

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.64→45.37 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.27 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17019 2605 5 %RANDOM
Rwork0.1482 ---
obs0.14933 49478 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.64→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 71 255 2597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212583
X-RAY DIFFRACTIONr_bond_other_d0.0010.021678
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9823506
X-RAY DIFFRACTIONr_angle_other_deg1.18434160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2132596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31615432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7491512
X-RAY DIFFRACTIONr_chiral_restr0.1570.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022936
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2741.51657
X-RAY DIFFRACTIONr_mcbond_other0.4351.5687
X-RAY DIFFRACTIONr_mcangle_it2.12222673
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4683926
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6434.5833
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: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 190 -
Rwork0.224 3599 -
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)
11.81120.51071.13260.64620.41351.7849-0.06710.18750.0058-0.04240.08110.0035-0.05720.2365-0.0140.02410.00010.00550.0628-0.00560.03026.64832.10915.529
20.65080.12080.05440.2065-0.10830.91680.03770.012-0.0390.02370.0112-0.0082-0.05570.066-0.04890.0514-0.0018-0.00180.0163-0.00050.0418-7.05225.93819.759
30.75850.1618-0.24476.1513-1.13982.34310.1672-0.08710.16340.3127-0.05360.0003-0.99080.0077-0.11360.4415-0.01130.07780.0228-0.03050.0482-18.59642.95230.206
41.52870.1364-0.67310.3647-0.01420.80370.1359-0.19760.02640.0697-0.08220.0066-0.10110.1046-0.05370.0446-0.0208-0.00740.0442-0.01330.0177-9.23926.95534.045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A405 - 487
2X-RAY DIFFRACTION2A488 - 597
3X-RAY DIFFRACTION3A598 - 661
4X-RAY DIFFRACTION4A662 - 717

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