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- PDB-9bc3: Transglutaminase 2 - Alternate state -

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Basic information

Entry
Database: PDB / ID: 9bc3
TitleTransglutaminase 2 - Alternate state
Components
  • HB-225 (gluten peptidomimetic TG2 inhibitor)
  • Protein-glutamine gamma-glutamyltransferase 2
KeywordsTRANSFERASE / Transglutaminase 2 / Alternate 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 / 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
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, 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: 2.52 Å
AuthorsMathews, I.I. / Sewa, A.S. / 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)P30GM133894 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
B: Protein-glutamine gamma-glutamyltransferase 2
C: HB-225 (gluten peptidomimetic TG2 inhibitor)
D: HB-225 (gluten peptidomimetic TG2 inhibitor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,3478
Polymers156,1874
Non-polymers1604
Water4,234235
1
A: Protein-glutamine gamma-glutamyltransferase 2
C: HB-225 (gluten peptidomimetic TG2 inhibitor)
hetero molecules


  • defined by author&software
  • 78.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)78,1744
Polymers78,0942
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-21 kcal/mol
Surface area19050 Å2
MethodPISA
2
B: Protein-glutamine gamma-glutamyltransferase 2
D: HB-225 (gluten peptidomimetic TG2 inhibitor)
hetero molecules


  • defined by author&software
  • 78.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)78,1744
Polymers78,0942
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-21 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.448, 71.416, 77.473
Angle α, β, γ (deg.)90.81, 107.19, 94.43
Int Tables number1
Space group name H-MP1

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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.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 1.57 Å3/Da / Density % sol: 21.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 4K, 10% 2-propanol, 0.1 M HEPES (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2022
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.52→39.11 Å / Num. obs: 26716 / % possible obs: 83.5 % / Redundancy: 2.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.092 / Rrim(I) all: 0.135 / Χ2: 0.84 / Net I/σ(I): 7.3
Reflection shellResolution: 2.52→2.66 Å / % possible obs: 82 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.416 / Num. measured all: 8421 / Num. unique obs: 3835 / CC1/2: 0.708 / Rpim(I) all: 0.383 / Rrim(I) all: 0.567 / Χ2: 0.79 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→39.11 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.856 / SU B: 21.324 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26452 1418 5.3 %RANDOM
Rwork0.20501 ---
obs0.20807 25297 83.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0.09 Å2-0.58 Å2
2--2.6 Å2-0.83 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2.52→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6866 0 104 235 7205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166546
X-RAY DIFFRACTIONr_angle_refined_deg0.941.8289710
X-RAY DIFFRACTIONr_angle_other_deg0.3591.78315042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.577552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58101130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021744
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_it0.7142.5973442
X-RAY DIFFRACTIONr_mcbond_other0.7142.5973442
X-RAY DIFFRACTIONr_mcangle_it1.3084.6664292
X-RAY DIFFRACTIONr_mcangle_other1.3084.6664293
X-RAY DIFFRACTIONr_scbond_it0.582.6573700
X-RAY DIFFRACTIONr_scbond_other0.582.6573701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0724.8575419
X-RAY DIFFRACTIONr_long_range_B_refined2.79325.527736
X-RAY DIFFRACTIONr_long_range_B_other2.76225.537717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.521→2.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 119 -
Rwork0.263 2002 -
obs--88.78 %
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)
10.12490.00160.10880.06280.09460.2869-0.0098-0.00550.0139-0.01170.0052-0.0059-0.0136-0.00640.00450.03390.00060.01870.00260.00240.05647.21641.89996.2567
20.1875-0.04880.13790.0874-0.0330.24460.0252-0.0522-0.0049-0.01110.00390.01560.007-0.0133-0.02910.0192-0.00320.0140.0226-0.00370.0521-20.9794-32.7285-2.7399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 447
2X-RAY DIFFRACTION2B1 - 447

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