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- PDB-4pyg: Transglutaminase2 complexed with GTP -

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Basic information

Entry
Database: PDB / ID: 4pyg
TitleTransglutaminase2 complexed with GTP
ComponentsProtein-glutamine gamma-glutamyltransferase 2Transglutaminase
KeywordsTRANSFERASE / Protein-GTP complex / Transglutaminase fold / Crosslinking / GTP binding / no modification
Function / homology
Function and homology information


histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase / positive regulation of mitochondrial calcium ion concentration / salivary gland cavitation / protein-glutamine gamma-glutamyltransferase activity / negative regulation of endoplasmic reticulum calcium ion concentration / dopamine secretion / peptide cross-linking / branching involved in salivary gland morphogenesis / cellular response to dopamine / positive regulation of small GTPase mediated signal transduction / Hydrolases; Acting on peptide bonds (peptidases) / apoptotic cell clearance / cellular response to cocaine / positive regulation of neurogenesis / positive regulation of cell adhesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / extracellular matrix / bone development / protein homooligomerization / positive regulation of GTPase activity / nucleosome / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / peptidase activity / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of apoptotic process / focal adhesion / calcium ion binding / chromatin / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / proteolysis / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. ...Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPark, H.H. / Jang, T.H.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of transglutaminase 2 with GTP complex and amino acid sequence evidence of evolution of GTP binding site.
Authors: Jang, T.H. / Lee, D.S. / Choi, K. / Jeong, E.M. / Kim, I.G. / Kim, Y.W. / Chun, J.N. / Jeon, J.H. / Park, H.H.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase 2
B: Protein-glutamine gamma-glutamyltransferase 2
E: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,0216
Polymers235,4523
Non-polymers1,5703
Water1,964109
1
A: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0072
Polymers78,4841
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0072
Polymers78,4841
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0072
Polymers78,4841
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.546, 216.218, 165.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

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Components

#1: Protein Protein-glutamine gamma-glutamyltransferase 2 / Transglutaminase / Tissue transglutaminase / Transglutaminase C / TG(C) / TGC / TGase C / Transglutaminase H / TGase H ...Tissue transglutaminase / Transglutaminase C / TG(C) / TGC / TGase C / Transglutaminase H / TGase H / Transglutaminase-2 / TGase-2


Mass: 78483.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20mM Mes pH 6.8, 200mM sodium chloride, 20mM MgCl2, 6% PEG 3350, 5mM DTT, 24% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2013
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 55587 / % possible obs: 25 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.92 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.863 / SU B: 20.685 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31904 2962 5.1 %RANDOM
Rwork0.23557 ---
all0.2842 ---
obs0.23985 55587 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16257 0 96 109 16462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216716
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.96722713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44452052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68824.328804
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.814152826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.84815117
X-RAY DIFFRACTIONr_chiral_restr0.1120.22502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112774
X-RAY DIFFRACTIONr_mcbond_it0.7641.510215
X-RAY DIFFRACTIONr_mcangle_it1.42216509
X-RAY DIFFRACTIONr_scbond_it1.56836501
X-RAY DIFFRACTIONr_scangle_it2.7084.56204
LS refinement shellResolution: 2.803→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 226 -
Rwork0.299 3953 -
obs--97.8 %

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