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- PDB-1vm8: Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (A... -

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Basic information

Entry
Database: PDB / ID: 1vm8
TitleCrystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution
ComponentsUDP-N-acetylglucosamine pyrophosphorylase
KeywordsTRANSFERASE / Agx2 / 16741099 / UDP-N-acetylglucosamine pyrophosphorylase / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


Synthesis of UDP-N-acetyl-glucosamine / protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / positive regulation of type I interferon production ...Synthesis of UDP-N-acetyl-glucosamine / protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / positive regulation of type I interferon production / antiviral innate immune response / carbohydrate binding / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Seminal Fluid Protein PDC-109 (Domain B) - #100 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Seminal Fluid Protein PDC-109 (Domain B) / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Ribbon / Alpha-Beta Complex ...Seminal Fluid Protein PDC-109 (Domain B) - #100 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Seminal Fluid Protein PDC-109 (Domain B) / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylhexosamine pyrophosphorylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE CLONING ARTIFACT: EXPERIMENTAL PHASING RESULTS REVEALED THAT RESIDUE 31 IS ... SEQUENCE CLONING ARTIFACT: EXPERIMENTAL PHASING RESULTS REVEALED THAT RESIDUE 31 IS SELENOMETHIONINE IN THE EXPRESSED CONSTRUCT AND NOT A VALINE AS PREDICTED BY THE SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine pyrophosphorylase
B: UDP-N-acetylglucosamine pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0599
Polymers121,7572
Non-polymers3017
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-46 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.094, 73.402, 107.132
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 2 - 516 / Label seq-ID: 14 - 528

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UDP-N-acetylglucosamine pyrophosphorylase


Mass: 60878.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: Q91YN5, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.25 %
Description: 1JV1 MODEL WAS USED TO GENERATE SE SITES FOR THREE WAVELENGTH MAD PHASING, WHICH WAS USED TO GENERATE RESTRAINTS FOR REFINEMENT.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 1.6M (NH4)2SO4, 0.1M Cacodylate pH 6.5, 0.2M NaCl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.9792
SYNCHROTRONALS 8.2.120.9792,1.0000,0.9791
DetectorType: ADSC / Detector: CCD / Date: Jun 5, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
211
30.97911
ReflectionResolution: 2.5→29.11 Å / Num. obs: 42134 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 54.17 Å2 / Rsym value: 0.073 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5964 / Rsym value: 0.402 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / SU B: 25.032 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.476 / ESU R Free: 0.297
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMS WITH INSUFFICIENT DENSITY HAVE NOT BEEN MODELED, INCLUDING REGIONS A453-476 AND B454-476.
RfactorNum. reflection% reflectionSelection details
Rfree0.26573 2124 5 %RANDOM
Rwork0.20676 ---
obs0.20971 39990 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.392 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å2-2.47 Å2
2---2.7 Å20 Å2
3---3.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 0 13 122 7639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227679
X-RAY DIFFRACTIONr_bond_other_d0.0010.026839
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.94610399
X-RAY DIFFRACTIONr_angle_other_deg0.794315864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0555975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70724.873355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.535151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4831531
X-RAY DIFFRACTIONr_chiral_restr0.0750.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021533
X-RAY DIFFRACTIONr_nbd_refined0.230.21771
X-RAY DIFFRACTIONr_nbd_other0.1820.27336
X-RAY DIFFRACTIONr_nbtor_other0.0880.24595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.29
X-RAY DIFFRACTIONr_mcbond_it1.87234979
X-RAY DIFFRACTIONr_mcbond_other0.40831994
X-RAY DIFFRACTIONr_mcangle_it2.51357773
X-RAY DIFFRACTIONr_scbond_it4.2883029
X-RAY DIFFRACTIONr_scangle_it6.11112626
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23860
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.22
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6982 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal0.712
LS refinement shellResolution: 2.5→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 141 4.81 %
Rwork0.305 2793 -
obs--94.46 %
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)
11.3601-0.12110.92381.05410.43291.31670.07610.166-0.1596-0.31440.06890.0316-0.1977-0.0253-0.1450.1053-0.0167-0.03040.08820.0169-0.040348.18636.76961.218
21.1175-0.763-0.28741.09920.45030.257-0.0194-0.0267-0.0053-0.154-0.03610.2458-0.0413-0.03290.0554-0.1665-0.0006-0.0001-0.04440.0126-0.090241.01945.633103.284
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 51714 - 529
22BB2 - 51614 - 528

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