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- PDB-9bc2: Transglutaminase 2 - Open State -

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Basic information

Entry
Database: PDB / ID: 9bc2
TitleTransglutaminase 2 - Open State
Components
  • HB-225 (gluten peptidomimetic TG2 inhibitor)
  • Protein-glutamine gamma-glutamyltransferase 2
KeywordsTRANSFERASE / Transglutaminase 2 / Open state
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 sprouting angiogenesis / 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 / 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
: / 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, 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMathews, I.I. / Sewa, A. / Khosla, C.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural and mechanistic analysis of Ca 2+ -dependent regulation of transglutaminase 2 activity using a Ca 2+ -bound intermediate state.
Authors: Sewa, A.S. / Besser, H.A. / Mathews, I.I. / Khosla, C.
History
DepositionApr 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
E: HB-225 (gluten peptidomimetic TG2 inhibitor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5137
Polymers78,0942
Non-polymers4205
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-71 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.609, 71.609, 309.780
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 Protein-glutamine gamma-glutamyltransferase 2 / Erythrocyte transglutaminase / Heart G alpha(h) / hhG alpha(h) / Isopeptidase TGM2 / Protein G ...Erythrocyte transglutaminase / Heart G alpha(h) / hhG alpha(h) / Isopeptidase TGM2 / Protein G alpha(h) / G(h) / Protein-glutamine deamidase TGM2 / Protein-glutamine dopaminyltransferase TGM2 / Protein-glutamine histaminyltransferase TGM2 / Protein-glutamine noradrenalinyltransferase TGM2 / Protein-glutamine serotonyltransferase TGM2 / Tissue transglutaminase / tTG / tTgase / Transglutaminase C / TG(C) / TGC / TGase C / Transglutaminase H / TGase H / Transglutaminase II / TGase II / Transglutaminase-2 / TG2 / TGase-2 / hTG2


Mass: 77412.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase, Hydrolases; Acting on peptide bonds (peptidases), protein-glutamine glutaminase, Transferases; Acyltransferases; Transferring ...References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase, Hydrolases; Acting on peptide bonds (peptidases), protein-glutamine glutaminase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide HB-225 (gluten peptidomimetic TG2 inhibitor)


Mass: 680.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 51.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 1.3-1.5M Ammonium Sulfate, 0.050 M Tris.HCl(pH8.9), 0.050M Bicine (pH 9)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→38.75 Å / Num. obs: 22176 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.407 / Rpim(I) all: 0.117 / Rrim(I) all: 0.424 / Χ2: 0.97 / Net I/σ(I): 7.7
Reflection shellResolution: 2.75→2.9 Å / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 3.602 / Num. measured all: 37421 / Num. unique obs: 3134 / CC1/2: 0.517 / Rpim(I) all: 1.075 / Rrim(I) all: 3.762 / Χ2: 0.9 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→38.75 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.862 / SU B: 23.875 / SU ML: 0.435 / Cross valid method: THROUGHOUT / ESU R: 9.392 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29916 1067 4.8 %RANDOM
Rwork0.2456 ---
obs0.2483 20968 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.747 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å2-0 Å2-0 Å2
2--2.86 Å2-0 Å2
3----5.72 Å2
Refinement stepCycle: 1 / Resolution: 2.75→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 0 71 66 5234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125277
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164919
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.8377170
X-RAY DIFFRACTIONr_angle_other_deg0.351.76511307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.277536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00510847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0430.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021222
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4636.6712594
X-RAY DIFFRACTIONr_mcbond_other2.4636.6712594
X-RAY DIFFRACTIONr_mcangle_it4.39511.9723232
X-RAY DIFFRACTIONr_mcangle_other4.39511.9733233
X-RAY DIFFRACTIONr_scbond_it2.0056.8072683
X-RAY DIFFRACTIONr_scbond_other26.7992668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.64512.4553915
X-RAY DIFFRACTIONr_long_range_B_refined7.43563.655569
X-RAY DIFFRACTIONr_long_range_B_other7.42463.665567
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.818 Å
RfactorNum. reflection% reflection
Rfree0.468 74 -
Rwork0.4 1465 -
obs--96.98 %

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