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- PDB-6a8p: Transglutaminase 2 mutant G224V in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 6a8p
TitleTransglutaminase 2 mutant G224V in complex with GTP
ComponentsProtein-glutamine gamma-glutamyltransferase 2
KeywordsTRANSFERASE / Transglutaminase / Complex / Mutant / GTP
Function / homology
Function and homology information


protein deamination / histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...protein deamination / histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase / positive regulation of mitochondrial calcium ion concentration / negative regulation of endoplasmic reticulum calcium ion concentration / salivary gland cavitation / protein-glutamine gamma-glutamyltransferase activity / dopamine secretion / branching involved in salivary gland morphogenesis / peptide cross-linking / cellular response to dopamine / positive regulation of small GTPase mediated signal transduction / apoptotic cell clearance / Hydrolases; Acting on peptide bonds (peptidases) / cellular response to cocaine / positive regulation of neurogenesis / positive regulation of sprouting angiogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of cell adhesion / extracellular matrix / positive regulation of GTPase activity / bone development / protein homooligomerization / nucleosome / peptidase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / 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 ...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: 2.537 Å
AuthorsPark, H.H. / Ha, H.J. / Kwon, S.
CitationJournal: PLoS ONE / Year: 2018
Title: Structure of natural variant transglutaminase 2 reveals molecular basis of gaining stability and higher activity.
Authors: Ha, H.J. / Kwon, S. / Jeong, E.M. / Kim, C.M. / Lee, K.B. / Kim, I.G. / Park, H.H.
History
DepositionJul 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)237,0216
Polymers235,4523
Non-polymers1,5703
Water00
1
A: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0072
Polymers78,4841
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0072
Polymers78,4841
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0072
Polymers78,4841
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.195, 216.312, 166.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein-glutamine gamma-glutamyltransferase 2 / Tissue transglutaminase / Transglutaminase C / TGase C / Transglutaminase H / TGase H / ...Tissue transglutaminase / Transglutaminase C / 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

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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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20 mM Mes (pH 6.8), 200 mM sodium chloride, 20 mM MgCl2, 6% PEG 3350, 5 mM DTT, 24% glycerol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.537→49.271 Å / Num. obs: 78019 / % possible obs: 99.6 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 19.8
Reflection shellResolution: 2.537→2.5659 Å / CC1/2: 0.741

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PYG

4pyg


Resolution: 2.537→49.271 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.54
RfactorNum. reflection% reflection
Rfree0.2575 4144 5.32 %
Rwork0.236 --
obs0.2371 77951 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.537→49.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15930 0 96 0 16026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716399
X-RAY DIFFRACTIONf_angle_d1.23522295
X-RAY DIFFRACTIONf_dihedral_angle_d13.6259789
X-RAY DIFFRACTIONf_chiral_restr0.0662462
X-RAY DIFFRACTIONf_plane_restr0.0072898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5371-2.56590.473820.37731514X-RAY DIFFRACTION62
2.5659-2.59610.35261330.33612534X-RAY DIFFRACTION100
2.5961-2.62780.35561300.33232434X-RAY DIFFRACTION100
2.6278-2.6610.36761370.33342492X-RAY DIFFRACTION100
2.661-2.69610.3421390.33082490X-RAY DIFFRACTION100
2.6961-2.7330.34341350.32772444X-RAY DIFFRACTION99
2.733-2.7720.34291530.34432452X-RAY DIFFRACTION99
2.772-2.81340.38691490.31762441X-RAY DIFFRACTION99
2.8134-2.85740.35161260.31842454X-RAY DIFFRACTION100
2.8574-2.90420.32951380.30542519X-RAY DIFFRACTION100
2.9042-2.95430.32591530.29682494X-RAY DIFFRACTION100
2.9543-3.0080.33851570.29232411X-RAY DIFFRACTION100
3.008-3.06580.33261570.29372492X-RAY DIFFRACTION100
3.0658-3.12840.33871250.30952504X-RAY DIFFRACTION100
3.1284-3.19640.29361330.29512496X-RAY DIFFRACTION100
3.1964-3.27070.30761270.26292509X-RAY DIFFRACTION100
3.2707-3.35250.29041420.26552467X-RAY DIFFRACTION100
3.3525-3.44310.27071570.262478X-RAY DIFFRACTION100
3.4431-3.54440.29461560.26262496X-RAY DIFFRACTION100
3.5444-3.65880.27851730.24062452X-RAY DIFFRACTION100
3.6588-3.78950.25921560.24422464X-RAY DIFFRACTION100
3.7895-3.94120.24991310.22642522X-RAY DIFFRACTION99
3.9412-4.12050.2551060.20882440X-RAY DIFFRACTION97
4.1205-4.33760.23731370.20122502X-RAY DIFFRACTION100
4.3376-4.60920.18931320.18072534X-RAY DIFFRACTION100
4.6092-4.96470.19211090.17652549X-RAY DIFFRACTION100
4.9647-5.46380.20241180.18972550X-RAY DIFFRACTION100
5.4638-6.25310.22211540.20362546X-RAY DIFFRACTION100
6.2531-7.8730.1831300.21832532X-RAY DIFFRACTION98
7.873-49.280.18121690.17672595X-RAY DIFFRACTION98

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