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- PDB-9yfk: Crystal Structure UTP--glucose-1-phosphate uridylyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 9yfk
TitleCrystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE (twinned lattice)
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / biosynthetic process
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE (twinned lattice)
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionSep 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1646
Polymers61,9832
Non-polymers1,1814
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-62 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.397, 71.027, 93.487
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase


Mass: 30991.625 Da / Num. of mol.: 2 / Fragment: 26-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: BP3403 / Plasmid: BopeA.00118.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7VTV0, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Berkeley B1: 30% PEG 3350, 400 mM NaCl, 100 mM Tris, pH 8.5. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. 2mM UTP, 2mM D-glucose-1-phosphate and 2mM MgCl2 added to protein prior to ...Details: Berkeley B1: 30% PEG 3350, 400 mM NaCl, 100 mM Tris, pH 8.5. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. 2mM UTP, 2mM D-glucose-1-phosphate and 2mM MgCl2 added to protein prior to crystallization. The product URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPG) was bound. plate 19925 B1 drop 3, Puck: PSL-0713, Cryo: 80% crystallant + 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 7, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.68→46.74 Å / Num. obs: 69602 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Χ2: 0.98 / Net I/σ(I): 12.2 / Num. measured all: 470183
Reflection shellResolution: 1.68→1.72 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.091 / Num. measured all: 35898 / Num. unique obs: 5172 / CC1/2: 0.553 / Rpim(I) all: 0.444 / Rrim(I) all: 1.18 / Χ2: 0.75 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5819: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→46.74 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2045 3370 4.84 %
Rwork0.1679 --
obs0.1777 69600 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 74 283 4587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094436
X-RAY DIFFRACTIONf_angle_d0.9576066
X-RAY DIFFRACTIONf_dihedral_angle_d14.6931738
X-RAY DIFFRACTIONf_chiral_restr0.056722
X-RAY DIFFRACTIONf_plane_restr0.009784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.28171860.2883345X-RAY DIFFRACTION95
1.71-1.740.26221210.29423369X-RAY DIFFRACTION96
1.74-1.770.26511750.27813227X-RAY DIFFRACTION95
1.77-1.810.2361690.28213314X-RAY DIFFRACTION95
1.81-1.850.2851560.27063280X-RAY DIFFRACTION95
1.85-1.890.27941650.26223315X-RAY DIFFRACTION95
1.89-1.940.28511790.25773269X-RAY DIFFRACTION94
1.94-1.990.26562170.23653262X-RAY DIFFRACTION94
1.99-2.050.28291790.23563276X-RAY DIFFRACTION95
2.05-2.120.25161480.23623306X-RAY DIFFRACTION95
2.12-2.190.24531560.2343318X-RAY DIFFRACTION95
2.19-2.280.23891530.2233358X-RAY DIFFRACTION95
2.28-2.380.24821450.2123261X-RAY DIFFRACTION95
2.38-2.510.21642040.21183311X-RAY DIFFRACTION94
2.51-2.670.23291690.20663339X-RAY DIFFRACTION95
2.67-2.870.19281510.19643307X-RAY DIFFRACTION95
2.87-3.160.2511730.18193298X-RAY DIFFRACTION95
3.16-3.620.19521650.15253334X-RAY DIFFRACTION95
3.62-4.560.17691690.11113322X-RAY DIFFRACTION95
4.56-46.740.15441800.11483429X-RAY DIFFRACTION95
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)
10.8766-0.01110.26570.64650.16910.9021-0.03160.02270.14190.04830.0162-0.0019-0.10990.05770.02550.20390.01350.01290.24180.00490.222915.07057.67048.7324
20.4671-0.24520.1030.9049-0.20760.6101-0.00580.0180.08160.03690.0176-0.13250.04710.136-0.00580.20740.02650.00150.3043-0.0140.234730.554-7.711215.0042
31.0643-0.273-0.29610.87410.25350.3956-0.0669-0.18890.01430.18920.0323-0.04470.04070.14830.05710.22980.0066-0.0130.2654-0.00010.193219.41893.842825.6009
42.42610.6930.07181.0517-0.10340.58070.10880.00570.34490.2035-0.01270.1298-0.0357-0.1363-0.09610.23020.01490.04160.2427-0.02580.2181-8.527611.007815.05
50.62730.03380.29770.5617-0.06950.81970.0468-0.0288-0.03460.0171-0.00490.07220.1109-0.0311-0.02840.2046-0.00640.0310.2487-0.01560.2137-11.35112.26715.3671
60.4387-0.07970.22710.5540.22810.79880.0145-0.01280.07070.0357-0.07810.136-0.0787-0.13180.06940.23460.00590.06890.2813-0.03520.2533-21.166820.10426.8465
71.1333-0.4310.0250.65190.00110.3361-0.0681-0.1670.02480.14950.0081-0.00220.0894-0.04250.05550.24630.00520.04370.2786-0.00630.2094-1.38745.289231.9903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 302 )
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 49 )
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 176 )
6X-RAY DIFFRACTION6chain 'B' and (resid 177 through 270 )
7X-RAY DIFFRACTION7chain 'B' and (resid 271 through 302 )

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