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- PDB-3eo3: Crystal structure of the N-acetylmannosamine kinase domain of hum... -

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Basic information

Entry
Database: PDB / ID: 3eo3
TitleCrystal structure of the N-acetylmannosamine kinase domain of human GNE protein
ComponentsBifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
KeywordsIsomerase / Transferase / non-protein kinase / sialic acid biosynthesis / Structural genomics consortium / SGC / Allosteric enzyme / ATP-binding / Disease mutation / Kinase / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein
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
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2.84 Å
AuthorsNedyalkova, L. / Tong, Y. / Rabeh, W.M. / Hong, B. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Tong, Y. / Rabeh, W.M. / Hong, B. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2009
Title: Crystal structure of the N-acetylmannosamine kinase domain of GNE.
Authors: Tong, Y. / Tempel, W. / Nedyalkova, L. / Mackenzie, F. / Park, H.W.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
B: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
C: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,25110
Polymers107,0553
Non-polymers1967
Water00
1
A: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules

B: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5017
Polymers71,3702
Non-polymers1315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3230 Å2
ΔGint-29 kcal/mol
Surface area23180 Å2
MethodPISA
2
C: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules

C: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5016
Polymers71,3702
Non-polymers1314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3180 Å2
ΔGint-31 kcal/mol
Surface area23240 Å2
MethodPISA
3
A: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
B: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5017
Polymers71,3702
Non-polymers1315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.946, 127.946, 127.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1-

UNX

DetailsACCORDING TO THE AUTHORS THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase / UDP-GlcNAc-2-epimerase/ManAc kinase / UDP-N-acetylglucosamine 2-epimerase / Uridine diphosphate-N- ...UDP-GlcNAc-2-epimerase/ManAc kinase / UDP-N-acetylglucosamine 2-epimerase / Uridine diphosphate-N-acetylglucosamine-2-epimerase / UDP-GlcNAc-2-epimerase / N-acetylmannosamine kinase / ManAc kinase


Mass: 35684.938 Da / Num. of mol.: 3 / Fragment: UNP residues 406-722
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNE, GLCNE / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9Y223, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing), N-acylmannosamine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8156.2
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, sitting drop5.615% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 5.6, vapor diffusion, sitting drop, temperature 291K
2912vapor diffusion, sitting drop614.55% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 6.0, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.97926
SYNCHROTRONAPS 19-ID20.97921
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 29, 2007
ADSC QUANTUM 3152CCDApr 10, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979211
ReflectionResolution: 2.84→30 Å / Num. obs: 29072 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.089 / Χ2: 1.88 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.84-2.9410.50.97828601.6071,2100
2.94-3.0611.10.67428791.6411,2100
3.06-3.211.30.47328511.5971,2100
3.2-3.3711.30.29928831.5661,2100
3.37-3.5811.30.18928741.7031,2100
3.58-3.8511.30.1229031.7731,2100
3.85-4.2411.20.08428881.9431,2100
4.24-4.8511.10.06729252.4231,2100
4.85-6.111.10.05729472.2611,2100
6.1-3010.60.03130622.2581,2100

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.8 Å / D res low: 20 Å / FOM : 0.3 / Reflection: 22643
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.9520.6720.0290.719
2Se600.8270.5210.0880.647
3Se600.1130.770.0820.637
4Se600.1140.570.0710.642
5Se600.010.4510.1730.574
6Se600.2440.9110.0380.794
7Se55.7680.9940.0330.0840.463
8Se600.8890.1010.0810.554
9Se600.2570.0510.0560.657
10Se600.5790.2210.030.564
11Se600.6750.4110.0530.454
12Se600.1370.3870.0370.432
Phasing MAD shell
Resolution (Å)FOM Reflection
9.38-200.421636
6.16-9.380.482525
4.89-6.160.443137
4.18-4.890.383546
3.7-4.180.293895
3.36-3.70.193741
3.1-3.360.113149
2.89-3.10.061014

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.84→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.189 / SU B: 35.648 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.707 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY. DUE TO TLS REFINEMENT, ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1071 3.726 %THIN SHELLS (SFTOOLS)
Rwork0.205 ---
obs0.207 28742 99.653 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.804 Å2
Baniso -1Baniso -2Baniso -3
1-0.212 Å20.106 Å20 Å2
2--0.212 Å20 Å2
3----0.317 Å2
Refinement stepCycle: LAST / Resolution: 2.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 7 0 5892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215966
X-RAY DIFFRACTIONr_bond_other_d0.0020.023548
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9698134
X-RAY DIFFRACTIONr_angle_other_deg0.8683.0028818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3875848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17325.674178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92715859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8531511
X-RAY DIFFRACTIONr_chiral_restr0.0630.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
X-RAY DIFFRACTIONr_mcbond_it0.81824213
X-RAY DIFFRACTIONr_mcbond_other0.11421774
X-RAY DIFFRACTIONr_mcangle_it1.45236596
X-RAY DIFFRACTIONr_scbond_it0.94221753
X-RAY DIFFRACTIONr_scangle_it1.55931538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.84-2.91300.3822092211798.819
2.913-2.99200.322003202299.06
2.992-3.0780.3671880.2881766196499.491
3.078-3.17200.2681924193799.329
3.172-3.2740.2981570.2571726188899.735
3.274-3.38800.2531782179299.442
3.388-3.5140.2861510.2261597175299.772
3.514-3.65600.2081698170399.706
3.656-3.8150.2531360.21470161099.752
3.815-3.99800.1861554155899.743
3.998-4.2110.2051140.17313571471100
4.211-4.4610.185840.17313251409100
4.461-4.76100.14913461346100
4.761-5.1320.176650.17511651230100
5.132-5.6050.329510.20411051156100
5.605-6.240.419150.23210381053100
6.24-7.1530.233190.21917936100
7.153-8.6390.214470.159765812100
8.639-11.7410.159250.147627652100
11.741-300.357190.22641443499.77
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)
11.7445-0.02780.78072.7963-0.3462.47190.04850.0920.0346-0.12540.18-0.1983-0.25030.2301-0.22840.2515-0.0429-0.04970.2969-0.20530.2075102.0927.435-2.383
23.8178-0.7789-0.23972.02570.37033.4528-0.0299-0.12240.8366-0.22460.09520.0488-0.7154-0.3678-0.06520.42880.1050.12780.33130.01230.417480.39919.512-45.193
34.72780.14270.58293.09070.17051.99930.0787-0.65910.63320.63-0.0109-0.1423-0.29530.0647-0.06770.2768-0.03380.01860.3229-0.06250.197952.1827.858-5.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A406 - 717
2X-RAY DIFFRACTION2B406 - 717
3X-RAY DIFFRACTION3C406 - 717

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