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- PDB-2q3z: Transglutaminase 2 undergoes large conformational change upon act... -

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Basic information

Entry
Database: PDB / ID: 2q3z
TitleTransglutaminase 2 undergoes large conformational change upon activation
Components
  • Polypeptide
  • Transglutaminase 2
KeywordsTRANSFERASE / Transglutaminase 2 / tissue transglutaminase / TG2
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
Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStrop, P. / Pinkas, D.M. / Brunger, A.T. / Khosla, C.
CitationJournal: Plos Biol. / Year: 2007
Title: Transglutaminase 2 undergoes a large conformational change upon activation
Authors: Pinkas, D.M. / Strop, P. / Brunger, A.T. / Khosla, C.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transglutaminase 2
X: Polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4467
Polymers77,9652
Non-polymers4805
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-68 kcal/mol
Surface area30630 Å2
MethodPISA, PQS
2
A: Transglutaminase 2
X: Polypeptide
hetero molecules

A: Transglutaminase 2
X: Polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,89114
Polymers155,9314
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9600 Å2
ΔGint-160 kcal/mol
Surface area56010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.671, 71.671, 309.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transglutaminase 2 / Tissue transglutaminase / TGase C / TGC / TGC / Transglutaminase-2 / TGase- H


Mass: 77341.602 Da / Num. of mol.: 1
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: Protein/peptide Polypeptide


Mass: 623.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized.
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 100 mM HEPES pH 7.25, 1.25M Amm. sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 53209 / Num. obs: 53209 / % possible obs: 94.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.072 / Χ2: 0.937 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.09 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.38 / Num. unique all: 5332 / Χ2: 0.905 / % possible all: 78.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KV3

1kv3


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.688 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.177 / Stereochemistry target values: Engh & Huber
Details: TLS group 1 1 to 462 TLS group 2 467 to 586 TLS group 3 587 to 683
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3482 6.3 %RANDOM
Rwork0.228 ---
obs0.231 53209 100 %-
all-53209 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.305 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.3 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5232 0 25 262 5519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225301
X-RAY DIFFRACTIONr_bond_other_d0.0020.023592
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9677205
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0038646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90424.074243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39815858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9471536
X-RAY DIFFRACTIONr_chiral_restr0.0850.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
X-RAY DIFFRACTIONr_nbd_refined0.1990.2964
X-RAY DIFFRACTIONr_nbd_other0.2020.23808
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22509
X-RAY DIFFRACTIONr_nbtor_other0.0880.23001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.10.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.218
X-RAY DIFFRACTIONr_mcbond_it0.8651.54188
X-RAY DIFFRACTIONr_mcbond_other0.1561.51327
X-RAY DIFFRACTIONr_mcangle_it1.04925260
X-RAY DIFFRACTIONr_scbond_it1.61432370
X-RAY DIFFRACTIONr_scangle_it2.344.51945
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 176 -
Rwork0.278 3616 -
obs-3792 100 %
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)
11.0255-0.11560.37871.0521-0.64714.42420.13810.0917-0.0928-0.2095-0.03020.03950.4482-0.191-0.1079-0.1153-0.0149-0.0203-0.33830-0.22659.935-0.21442.759
21.9538-0.73291.5676.0188-0.31078.7493-0.07250.12470.0971-0.06630.15240.0587-0.25860.0487-0.07980.06070.07740.0045-0.23980.0484-0.205614.532-13.922-1.866
34.6191.3771.001713.2923-3.420410.9320.17570.6371-1.0205-0.585-0.019-0.53671.1731-0.2586-0.15670.20390.0248-0.15160.0346-0.02850.15657.107-19.093-38.952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4611 - 461
2X-RAY DIFFRACTION2AA472 - 586472 - 586
3X-RAY DIFFRACTION3AA587 - 683587 - 683

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