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- PDB-4ap6: Crystal structure of human POFUT2 E54A mutant in complex with GDP... -

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Basic information

Entry
Database: PDB / ID: 4ap6
TitleCrystal structure of human POFUT2 E54A mutant in complex with GDP- fucose
ComponentsGDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
KeywordsTRANSFERASE / GT-B / GT68
Function / homology
Function and homology information


positive regulation of protein folding / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / regulation of secretion / O-glycosylation of TSR domain-containing proteins / fucose metabolic process / regulation of epithelial to mesenchymal transition / mesoderm formation / regulation of gene expression ...positive regulation of protein folding / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / regulation of secretion / O-glycosylation of TSR domain-containing proteins / fucose metabolic process / regulation of epithelial to mesenchymal transition / mesoderm formation / regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus
Similarity search - Function
GDP-fucose protein O-fucosyltransferase 2-like / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / GDP-fucose protein O-fucosyltransferase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.401 Å
AuthorsChen, C. / Keusch, J.J. / Klein, D. / Hess, D. / Hofsteenge, J. / Gut, H.
CitationJournal: Embo J. / Year: 2012
Title: Structure of Human Pofut2: Insights Into Thrombospondin Type 1 Repeat Fold and O-Fucosylation.
Authors: Chen, C.I. / Keusch, J.J. / Klein, D. / Hess, D. / Hofsteenge, J. / Gut, H.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
B: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
C: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
D: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,04218
Polymers198,2164
Non-polymers3,82614
Water1448
1
A: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4004
Polymers49,5541
Non-polymers8463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8426
Polymers49,5541
Non-polymers1,2885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6215
Polymers49,5541
Non-polymers1,0674
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1793
Polymers49,5541
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.010, 153.010, 185.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 43:90 OR RESSEQ 100:295 OR RESSEQ...
211CHAIN B AND (RESSEQ 43:90 OR RESSEQ 100:295 OR RESSEQ...
311CHAIN C AND (RESSEQ 43:90 OR RESSEQ 100:295 OR RESSEQ...
411CHAIN D AND (RESSEQ 43:90 OR RESSEQ 100:295 OR RESSEQ...
112CHAIN A AND RESSEQ 1430
212CHAIN B AND RESSEQ 1430
312CHAIN C AND RESSEQ 1430
412CHAIN D AND RESSEQ 1430

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.4947, 0.869, 0.006606), (-0.3035, 0.1799, -0.9357), (-0.8143, 0.4609, 0.3528)64.04, 0.1922, 30.51
2given(-0.01399, 0.5964, -0.8026), (0.6138, -0.6285, -0.4777), (-0.7893, -0.4993, -0.3573)96.79, -45.57, -12.07
3given(0.5757, -0.162, -0.8014), (0.8108, 0.2397, 0.534), (0.1056, -0.9572, 0.2693)79.06, -23.04, -69.35

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Components

#1: Protein
GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2 / PEPTIDE-O-FUCOSYLTRANSFERASE 2 / O-FUCT-2 / PROTEIN O-FUCOSYLTRANSFERASE 2


Mass: 49553.961 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-429 / Mutation: YES [E54A]
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y2G5, peptide-O-fucosyltransferase
#2: Chemical
ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 54 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 54 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 54 TO ALA

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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: 3.2 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.2M NASCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DUAL CHANNEL CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 32751 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 77.22 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11
Reflection shellResolution: 3.4→3.63 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.1 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.401→39.686 Å / SU ML: 0.89 / σ(F): 1.99 / Phase error: 22 / Stereochemistry target values: ML
Details: RESIDUES 298-302 ARE PARTIALLY DISORDERED. CHAIN D IS EITHER HIGHLY MOBILE OR NOT FULLY OCCUPIED IN THE CRYSTAL.
RfactorNum. reflection% reflection
Rfree0.238 1622 4.9 %
Rwork0.1924 --
obs0.1947 32745 93.55 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.003 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2146 Å20 Å20 Å2
2--2.2146 Å20 Å2
3----4.4293 Å2
Refinement stepCycle: LAST / Resolution: 3.401→39.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12974 0 240 8 13222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113605
X-RAY DIFFRACTIONf_angle_d1.29218456
X-RAY DIFFRACTIONf_dihedral_angle_d18.2765068
X-RAY DIFFRACTIONf_chiral_restr0.0941919
X-RAY DIFFRACTIONf_plane_restr0.0062331
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3085X-RAY DIFFRACTIONPOSITIONAL
12B3085X-RAY DIFFRACTIONPOSITIONAL0.054
13C3085X-RAY DIFFRACTIONPOSITIONAL0.06
14D3085X-RAY DIFFRACTIONPOSITIONAL0.05
21A38X-RAY DIFFRACTIONPOSITIONAL
22B38X-RAY DIFFRACTIONPOSITIONAL0.028
23C38X-RAY DIFFRACTIONPOSITIONAL0.031
24D38X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4014-3.50150.29491320.28532499X-RAY DIFFRACTION93
3.5015-3.61440.31691060.26482675X-RAY DIFFRACTION96
3.6144-3.74350.31071390.24762613X-RAY DIFFRACTION96
3.7435-3.89320.29911400.23572605X-RAY DIFFRACTION95
3.8932-4.07030.26351400.2072600X-RAY DIFFRACTION95
4.0703-4.28460.25911380.17662602X-RAY DIFFRACTION95
4.2846-4.55270.19771420.16052604X-RAY DIFFRACTION94
4.5527-4.90360.21390.14282606X-RAY DIFFRACTION94
4.9036-5.3960.20211310.16042565X-RAY DIFFRACTION93
5.396-6.17430.22611400.18772596X-RAY DIFFRACTION92
6.1743-7.76940.23381390.18272562X-RAY DIFFRACTION91
7.7694-39.68870.20441360.17862596X-RAY DIFFRACTION89
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)
12.22420.0895-0.43124.33190.67764.9894-0.17930.12070.1836-0.1970.2317-0.3-0.48410.3695-0.01920.6263-0.21840.14120.6814-0.17970.719918.67949.004615.6273
22.97221.3540.72316.20790.20722.7025-0.1460.2812-0.259-0.45760.3217-0.7922-0.0010.5069-0.10850.5378-0.01730.2120.7703-0.30670.778621.1672-18.09635.0223
35.3518-0.5960.02192.4709-0.07093.49020.1791-0.0242-0.0905-0.162-0.0984-0.0094-0.0785-0.3305-0.06720.5570.12610.0620.4266-0.03880.3733-13.0105-44.6988-13.7788
44.8163-0.6917-0.99285.8506-0.86524.69450.1147-0.5085-0.44550.1546-0.0322-0.38070.1240.2107-0.12010.35270.064-0.10040.6128-0.03180.47375.0856-52.27437.8356
53.70790.28230.73425.2068-0.23353.57250.10910.1597-0.3281-0.14780.11440.46610.2648-0.3462-0.16840.5799-0.0831-0.22140.89470.12620.516812.7115-94.724426.73
67.4011-0.017-0.72873.334-0.00047.8060.0584-0.19320.15150.56130.15420.4838-0.5589-0.2936-0.19430.77930.0384-0.00790.58370.16030.66474.5596-70.724441.4416
74.59270.4161.08823.7135-1.37781.5651-0.4297-0.37780.85530.62980.3294-0.3923-1.810.03360.09452.41-0.20160.17150.7628-0.00561.24450.1885-63.914188.3988
84.06441.67480.4967.7212-0.72442.3087-0.28830.13441.0597-0.59940.33931.078-1.8181-0.6786-0.09672.12740.35580.08661.02480.31081.3195-21.4435-60.628969.0557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 41:243)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 244:429)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 41:243)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 244:429)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 41:243)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 244:429)
7X-RAY DIFFRACTION7CHAIN D AND (RESSEQ 41:243)
8X-RAY DIFFRACTION8CHAIN D AND (RESSEQ 244:429)

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