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- PDB-9iis: GDP-fucose pyrophosphorylase part of FKP with a SUMO tag -

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Basic information

Entry
Database: PDB / ID: 9iis
TitleGDP-fucose pyrophosphorylase part of FKP with a SUMO tag
ComponentsUbiquitin-like protein SMT3,L-fucokinase/L-fucose-1-P guanylyltransferase
KeywordsTRANSFERASE / GDP-fucose / pyrophosphorylase / HEPES / beta-helix / SUMO
Function / homology
Function and homology information


fucokinase / fucose-1-phosphate guanylyltransferase / fucokinase activity / GDP-L-fucose salvage / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors ...fucokinase / fucose-1-phosphate guanylyltransferase / fucokinase activity / GDP-L-fucose salvage / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / nucleotidyltransferase activity / condensed nuclear chromosome / protein tag activity / ATP binding / identical protein binding / nucleus
Similarity search - Function
L-fucokinase / Fucose pyrophosphorylase domain / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Rad60/SUMO-like domain ...L-fucokinase / Fucose pyrophosphorylase domain / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ACETATE ION / Ubiquitin-like protein SMT3 / L-fucokinase/L-fucose-1-P guanylyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Bacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.36 Å
AuthorsKo, T.P. / Lin, S.W. / Hsu, M.F. / Lin, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural insight into the catalytic mechanism of the bifunctional enzyme l-fucokinase/GDP-fucose pyrophosphorylase.
Authors: Lin, S.W. / Ko, T.P. / Chiang, H.Y. / Wu, C.G. / Hsu, M.F. / Wang, A.H. / Lin, C.H.
History
DepositionJun 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,L-fucokinase/L-fucose-1-P guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0793
Polymers69,7811
Non-polymers2972
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint2 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.585, 109.854, 144.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1117-

HOH

21A-1227-

HOH

31A-1247-

HOH

41A-1304-

HOH

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Components

#1: Protein Ubiquitin-like protein SMT3,L-fucokinase/L-fucose-1-P guanylyltransferase


Mass: 69781.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GDP-fucose pyrophosphorylase part of FKP with a SUMO tag
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Bacteroides fragilis (bacteria)
Gene: SMT3, fkp / Plasmid: pET-SUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q12306, UniProt: Q58T34
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, ammonium acetate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 28528 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 56.51 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2831 / CC1/2: 0.893 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Blu-Icedata collection
RefinementMethod to determine structure: SAD / Resolution: 2.36→29.12 Å / SU ML: 0.2921 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.8686
RfactorNum. reflection% reflection
Rfree0.2539 1422 5 %
Rwork0.2026 --
obs0.2052 28436 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 93.08 Å2
Refinement stepCycle: LAST / Resolution: 2.36→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 0 227 4617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264491
X-RAY DIFFRACTIONf_angle_d0.64956074
X-RAY DIFFRACTIONf_chiral_restr0.0444662
X-RAY DIFFRACTIONf_plane_restr0.005778
X-RAY DIFFRACTIONf_dihedral_angle_d16.32762698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.440.33361370.29542584X-RAY DIFFRACTION95.54
2.44-2.540.27841420.27032669X-RAY DIFFRACTION99.22
2.54-2.650.32841410.25642683X-RAY DIFFRACTION99.51
2.65-2.790.32061410.24022701X-RAY DIFFRACTION99.41
2.79-2.970.32981410.25742694X-RAY DIFFRACTION99.51
2.97-3.20.34281420.24472710X-RAY DIFFRACTION99.89
3.2-3.520.29181430.22012722X-RAY DIFFRACTION99.72
3.52-4.030.2541450.18982744X-RAY DIFFRACTION99.79
4.03-5.070.19031430.16592733X-RAY DIFFRACTION99.04
5.07-29.120.22571470.18292774X-RAY DIFFRACTION96.15
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)
10.2186072137010.1182061954140.3161081535310.3001306903060.08028720091840.7440879321470.14759990515-0.6299641488831.30616836953-0.2767466086390.0267573872768-0.08374027953-0.31013946248-0.6433337192860.07481229950921.044933030140.005045582589210.04450090006480.66698138708-0.2239586993861.6536483700225.47247531922.4617539976818.5817429511
21.93582775337-0.0494805481069-0.368673186982.13123800409-0.1779736845211.39361018270.142823956191-0.761917137879-0.1346401946470.1630066552960.03872241368980.0942235100958-0.170103210835-0.1450127808890.0001443834332770.454060438526-0.131773277535-0.005199136797040.7175938322030.1157698726680.48492122821951.280235324123.854742183829.9497810226
32.320915826480.224344839732-1.111799351951.5152087243-0.2954785601612.017459591340.1656280747740.2278837992260.341012311616-0.0330721957591-0.118327223798-0.0114301772047-0.0115154706920.214066086261.12462723624E-50.49066731640.005163796523730.01134926662080.464407673970.06114209951170.48390557337967.761613662837.37019669035.14989759511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -78 through -3 )
2X-RAY DIFFRACTION2chain 'A' and (resid -2 through 290 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 492 )

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