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- PDB-7nuu: Crystal structure of human AMDHD2 in complex with Zn -

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Basic information

Entry
Database: PDB / ID: 7nuu
TitleCrystal structure of human AMDHD2 in complex with Zn
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsHYDROLASE / N-acetylglucosamine-6-phosphate deacetylase / NagA / Amidohydrolase domain-containing protein 2 / AMDHD2
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase / N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / Synthesis of UDP-N-acetyl-glucosamine / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate metabolic process / nucleus / metal ion binding / cytosol
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.836 Å
AuthorsRuegenberg, S. / Kroef, V. / Baumann, U. / Denzel, M.S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research01GQ1423A Germany
European CommissionERC-2014-StG-640254-MetAGEn Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
Citation
Journal: Elife / Year: 2022
Title: GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway.
Authors: Kroef, V. / Ruegenberg, S. / Horn, M. / Allmeroth, K. / Ebert, L. / Bozkus, S. / Miethe, S. / Elling, U. / Schermer, B. / Baumann, U. / Denzel, M.S.
#1: Journal: Biorxiv / Year: 2021
Title: GFAT2 and AMDHD2 act in tandem to control the hexosamine biosynthetic pathway
Authors: Kroef, V. / Ruegenberg, S. / Horn, M. / Allmeroth, K. / Ebert, L. / Bozkus, S. / Miethe, S. / Schermer, B. / Baumann, U. / Denzel, M.S.
History
DepositionMar 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9236
Polymers87,6082
Non-polymers3154
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-92 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.777, 84.336, 154.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 254 or (resid 255...
21(chain B and (resid 10 through 404 or (resid 405...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 10 through 254 or (resid 255...A10 - 254
121(chain A and (resid 10 through 254 or (resid 255...A255
131(chain A and (resid 10 through 254 or (resid 255...A8 - 501
141(chain A and (resid 10 through 254 or (resid 255...A8 - 501
151(chain A and (resid 10 through 254 or (resid 255...A8 - 501
161(chain A and (resid 10 through 254 or (resid 255...A8 - 501
211(chain B and (resid 10 through 404 or (resid 405...B0

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Components

#1: Protein N-acetylglucosamine-6-phosphate deacetylase / GlcNAc 6-P deacetylase / Amidohydrolase domain-containing protein 2


Mass: 43803.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMDHD2, CGI-14 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y303, N-acetylglucosamine-6-phosphate deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 8.25, 0.25 M Sodium nitrate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.836→77.083 Å / Num. obs: 71036 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 12.53
Reflection shellResolution: 1.836→1.902 Å / Num. unique obs: 6953 / CC1/2: 0.499

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NUT

7nut


Resolution: 1.836→77.083 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1992 2.8 %
Rwork0.1823 69033 -
obs0.183 71025 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122 Å2 / Biso mean: 41.6033 Å2 / Biso min: 18.56 Å2
Refinement stepCycle: final / Resolution: 1.836→77.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5999 0 28 318 6345
Biso mean--47.82 35.7 -
Num. residues----797
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3598X-RAY DIFFRACTION9.278TORSIONAL
12B3598X-RAY DIFFRACTION9.278TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8363-1.88220.32721390.3191482799
1.8822-1.93310.31531400.28884861100
1.9331-1.990.26931400.26564859100
1.99-2.05420.27181410.24414903100
2.0542-2.12770.24611410.23484867100
2.1277-2.21280.25841420.20984905100
2.2128-2.31360.23571390.19764863100
2.3136-2.43550.22511420.18674913100
2.4355-2.58820.20891420.1844922100
2.5882-2.7880.20551420.18234936100
2.788-3.06860.21631430.17864945100
3.0686-3.51260.18181440.16894991100
3.5126-4.42550.15941450.14635013100
4.4255-77.0830.1911520.1645228100
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)
13.0610.15231.24262.8926-1.48078.09890.09010.35940.0099-0.37360.15120.22390.5227-0.3223-0.24630.4359-0.0803-0.10580.37250.01870.3073-9.6594-13.3733.6529
21.76280.41480.47211.5170.21491.6379-0.02950.1543-0.0133-0.2860.0498-0.16940.16460.2421-0.02220.28770.02280.03480.21210.01440.242814.2203-11.024824.8875
37.48882.2652-1.17741.8319-0.24461.45430.043-0.16840.32420.0162-0.06880.3248-0.0376-0.12930.00050.21070.0369-0.0340.3263-0.01620.3517-36.3812-5.616854.4842
42.3822-0.7076-1.00391.56870.66991.8202-0.1419-0.474-0.10410.29670.1212-0.02720.24970.26960.00930.20180.0161-0.02070.24520.05340.1699-6.5132-13.709362.3521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 56 )A10 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 405 )A57 - 405
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 56 )B10 - 56
4X-RAY DIFFRACTION4chain 'B' and (resid 57 through 407 )B57 - 407

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