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- PDB-2yi1: Crystal structure of N-Acetylmannosamine kinase in complex with N... -

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Basic information

Entry
Database: PDB / ID: 2yi1
TitleCrystal structure of N-Acetylmannosamine kinase in complex with N- acetyl mannosamine 6-phosphate and ADP.
ComponentsBIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE
KeywordsTRANSFERASE / SUGAR KINASE / 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-acetylneuraminate biosynthetic process / N-acylmannosamine kinase activity / N-acylmannosamine kinase / CMP-N-acetylneuraminate biosynthetic process / glycosylation / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process ...Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acetylneuraminate biosynthetic process / N-acylmannosamine kinase activity / N-acylmannosamine kinase / CMP-N-acetylneuraminate biosynthetic process / glycosylation / 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 / ADENOSINE-5'-DIPHOSPHATE / 2-acetamido-2-deoxy-alpha-D-mannopyranose / Chem-BMX / Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMartinez, J. / Nguyen, L.D. / Tauberger, E. / Hinderlich, S. / Reutter, W. / Fan, H. / Saenger, W. / 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 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Other
Revision 1.2May 2, 2012Group: Other
Revision 1.3Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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_label_alt_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_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 1.4Dec 20, 2023Group: 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: BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,67515
Polymers36,6391
Non-polymers2,03514
Water2,576143
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)77,34930
Polymers73,2782
Non-polymers4,07128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9210 Å2
ΔGint-59.9 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.700, 90.700, 101.490
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 , 1 types, 1 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: 36639.016 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)-RIL / References: UniProt: Q9Y223, N-acylmannosamine kinase

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-BMX / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose / 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE / N-acetyl-6-O-phosphono-alpha-D-mannosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-ManpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: 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 , 9 types, 155 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2-(ACETYLAMINO)-6-(PHOSPHATE)-2-DEOXY-ALPHA-D-MANNOPYRANOSE (BMX): N ACETYL MANNOSAMINE ...2-(ACETYLAMINO)-6-(PHOSPHATE)-2-DEOXY-ALPHA-D-MANNOPYRANOSE (BMX): N ACETYL MANNOSAMINE PHOSPHORYLATED AT THE C6 POSITION.

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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: 2.85 Å3/Da / Density % sol: 56.82 % / Description: NONE
Crystal growDetails: 0.2 M CALCIUM ACETATE, 0.1M 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.1→41.4 Å / Num. obs: 24925 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YHW

2yhw


Resolution: 2.15→41.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.828 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19101 1179 5 %RANDOM
Rwork0.16667 ---
obs0.16791 22395 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: 37.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 117 143 2530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212517
X-RAY DIFFRACTIONr_bond_other_d0.0010.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.7882.0033416
X-RAY DIFFRACTIONr_angle_other_deg1.01434028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2852590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25215414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7511510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02447
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_it0.9761.51587
X-RAY DIFFRACTIONr_mcbond_other0.2891.5664
X-RAY DIFFRACTIONr_mcangle_it1.75622549
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0073930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8084.5867
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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 86 -
Rwork0.177 1630 -
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)
10.4857-0.26610.00491.5158-0.33211.30350.0330.0048-0.0713-0.13960.0105-0.01670.19680.0628-0.04350.05970.00580.00430.07640.00540.084128.8131.134-7.126
246.068-5.35884.87053.5962.305320.8076-0.7437-0.58981.06590.26740.0437-0.7381-0.08293.14930.69990.1286-0.0237-0.07441.1530.10710.498850.16718.3894.739
30.6696-0.4012-0.25642.48621.02611.7306-0.0887-0.1682-0.02760.26420.1249-0.05590.11060.1836-0.03620.05240.0154-0.02020.08980.01650.055426.76411.8798.034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A405 - 597
2X-RAY DIFFRACTION2A598 - 642
3X-RAY DIFFRACTION3A643 - 717

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