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- PDB-3ly6: Crystal structure of human transglutaminase 2 complex with adenos... -

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Basic information

Entry
Database: PDB / ID: 3ly6
TitleCrystal structure of human transglutaminase 2 complex with adenosine 5' Triphosphate
ComponentsProtein-glutamine gamma-glutamyltransferase 2
KeywordsTRANSFERASE / transglutaminase / Acyltransferase / Diabetes mellitus / Disease mutation / Metal-binding / Phosphoprotein
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 / apoptotic cell clearance / Hydrolases; Acting on peptide bonds (peptidases) / cellular response to cocaine / positive regulation of neurogenesis / positive regulation of cell adhesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / extracellular matrix / positive regulation of GTPase activity / bone development / protein homooligomerization / nucleosome / phospholipase C-activating G protein-coupled receptor signaling pathway / peptidase activity / gene expression / regulation of apoptotic process / collagen-containing extracellular matrix / 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
ADENOSINE-5'-TRIPHOSPHATE / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsHan, B.G. / Lee, B.I.
CitationJournal: Int.J.Biol.Macromol. / Year: 2010
Title: Crystal structure of human transglutaminase 2 in complex with adenosine triphosphate
Authors: Han, B.G. / Cho, J.W. / Cho, Y.D. / Jeong, K.C. / Kim, S.Y. / Lee, B.I.
History
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,6766
Polymers236,1543
Non-polymers1,5223
Water00
1
A: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2252
Polymers78,7181
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2252
Polymers78,7181
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2252
Polymers78,7181
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.175, 215.759, 165.956
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 / TGM2 / Tissue transglutaminase / TGase C / TGC / TG(C) / Transglutaminase-2 / TGase-H


Mass: 78718.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Plasmid: pET32 (Novagen) / Production host: Escherichia coli (E. coli)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Sequence detailsTHIS SEQUENCE IS FROM GENBANK, AAA63261. SEE REFERENCE 1 IN UNP DATABASE, P21980.

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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: 51.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 50MM MES, 200MM NACL, 50MM MGCL2, 6-8% PEG3350,5MM DTT, 20% GLYCEROL, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. all: 42242 / Num. obs: 41905 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.14→3.26 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KV3

1kv3


Resolution: 3.14→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2969 3927 RANDOM
Rwork0.2333 --
obs0.2333 38955 -
all-42310 -
Refinement stepCycle: LAST / Resolution: 3.14→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16203 0 93 0 16296

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