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- PDB-7nut: Crystal structure of human AMDHD2 in complex with Zn and GlcN6P -

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Basic information

Entry
Database: PDB / ID: 7nut
TitleCrystal structure of human AMDHD2 in complex with Zn and GlcN6P
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsHYDROLASE / N-acetylglucosamine-6-phosphate deacetylase / NagA / Amidohydrolase domain-containing protein 2 / AMDHD2
Function / homology
Function and homology information


negative regulation of UDP-N-acetylglucosamine biosynthetic process / N-acetylglucosamine-6-phosphate deacetylase / N-acetylglucosamine-6-phosphate deacetylase activity / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / metal ion binding / nucleus / 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
Chem-GLP / N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 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 / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)88,2576
Polymers87,6082
Non-polymers6494
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-99 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.261, 161.449, 86.621
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 9 through 84 or (resid 85...
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTHRTHR(chain A and (resid 9 through 84 or (resid 85...AA9 - 849 - 84
12GLUGLUGLUGLU(chain A and (resid 9 through 84 or (resid 85...AA8585
13GLYGLYHOHHOH(chain A and (resid 9 through 84 or (resid 85...AA - G6 - 6016
14GLYGLYHOHHOH(chain A and (resid 9 through 84 or (resid 85...AA - G6 - 6016
15GLYGLYHOHHOH(chain A and (resid 9 through 84 or (resid 85...AA - G6 - 6016
16GLYGLYHOHHOH(chain A and (resid 9 through 84 or (resid 85...AA - G6 - 6016
21GLYGLYALAALAchain BBB9 - 4069 - 406

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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: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.28 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→48.707 Å / Num. obs: 70760 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 11.46
Reflection shellResolution: 1.898→1.97 Å / Num. unique obs: 6907 / CC1/2: 0.494

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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: 2VHL

2vhl


Resolution: 1.898→48.707 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 1981 2.8 %
Rwork0.185 68773 -
obs0.1857 70754 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.87 Å2 / Biso mean: 47.8538 Å2 / Biso min: 23.93 Å2
Refinement stepCycle: final / Resolution: 1.898→48.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5997 0 58 330 6385
Biso mean--45.31 40.1 -
Num. residues----799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3584X-RAY DIFFRACTION6.021TORSIONAL
12B3584X-RAY DIFFRACTION6.021TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.898-1.9450.32171360.3227471797
1.945-1.99760.2781400.30264828100
1.9976-2.05640.30171400.28494883100
2.0564-2.12270.33021400.264857100
2.1227-2.19860.27061400.23684876100
2.1986-2.28660.23151390.21024872100
2.2866-2.39070.20221410.18754890100
2.3907-2.51670.20511420.18584913100
2.5167-2.67440.19751400.1854885100
2.6744-2.88090.21291430.19184940100
2.8809-3.17070.24431420.18924926100
3.1707-3.62940.20961430.17714951100
3.6294-4.57220.17611450.14725036100
4.5722-48.7070.18941500.1614519999
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)
11.4103-0.89970.05543.15240.91662.13510.0801-0.04830.3233-0.3281-0.14310.2757-0.8613-0.54860.07720.63630.18880.00810.5907-0.01040.4996-25.170435.7299-33.7876
20.8557-0.32680.03931.5025-0.10181.56950.0355-0.0190.1181-0.063-0.0049-0.1803-0.27660.2035-0.02450.3002-0.06150.02020.3253-0.0220.2899-1.541413.757-31.5481
33.23840.32731.03980.27910.36491.0521-0.0639-0.1085-0.0473-0.06060.0620.24430.0648-0.5023-0.02330.384-0.0210.00670.62060.08570.5616-52.4357-16.7273-28.1261
41.82670.4576-0.75821.2648-0.45081.6407-0.070.0234-0.2608-0.10430.0663-0.0320.36850.0258-0.00550.3195-0.0036-0.04010.2515-0.01420.3009-22.1525-23.7209-35.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 56 )A6 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 406 )A57 - 406
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 56 )B9 - 56
4X-RAY DIFFRACTION4chain 'B' and (resid 57 through 406 )B57 - 406

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