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- PDB-3s3s: Transglutaminase 2 in complex with a novel inhibitor -

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Basic information

Entry
Database: PDB / ID: 3s3s
TitleTransglutaminase 2 in complex with a novel inhibitor
Components
  • Protein-glutamine gamma-glutamyltransferase 2Transglutaminase
  • peptide inhibitor
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transglutaminase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 cell adhesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / extracellular matrix / bone development / protein homooligomerization / positive regulation of GTPase activity / nucleosome / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / peptidase activity / 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 / 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
N-[(2R)-2-{[(benzyloxy)carbonyl]amino}-7-ethoxy-7-oxoheptanoyl]-L-valyl-L-prolyl-L-leucine / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsLindemann, I. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Inhibitors of Transglutaminase 2: A therapeutic option in celiac disease
Authors: Lindemann, I. / Boettcher, J. / Oertel, K. / Weber, J. / Hils, M. / Pasternack, R. / Heine, A. / Klebe, G.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Sep 13, 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_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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,5548
Polymers78,9782
Non-polymers5766
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.439, 71.439, 310.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE MAIN POLYMERIC PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE 2 IS A MONOMER IN THE ABSENCE OF THE PEPTIDE INHIBITOR

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Components

#1: Protein Protein-glutamine gamma-glutamyltransferase 2 / Transglutaminase / Tissue transglutaminase / Transglutaminase C / TG(C) / TGC / TGase C / Transglutaminase H / TGase H ...Tissue transglutaminase / Transglutaminase C / TG(C) / TGC / TGase C / Transglutaminase H / TGase H / Transglutaminase-2 / TGase-2


Mass: 78312.641 Da / Num. of mol.: 1 / Fragment: unp residues 2-687
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 peptide inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 665.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-[(2R)-2-{[(benzyloxy)carbonyl]amino}-7-ethoxy-7-oxoheptanoyl]-L-valyl-L-prolyl-L-leucine
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNREACTED FORM OF THE PEPTIDE INHIBITOR, CHAIN B HAS A DOUBLE BOND BETWEEN C15 AND C17 OF THE ...THE UNREACTED FORM OF THE PEPTIDE INHIBITOR, CHAIN B HAS A DOUBLE BOND BETWEEN C15 AND C17 OF THE AMINOACID XW1. UPON REACTION WITH PROTEIN, A COVALENT BOND BETWEEN C15 AND SG OF CYS 277 CHAIN A IS FORMED

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.0 M Amm. sulfate, 0.1 M HEPES, VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 21, 2010 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 34641 / Num. obs: 34641 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.075 / Net I/σ(I): 23.5
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2006 / Rsym value: 0.345 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q3z

2q3z


Resolution: 2.301→48.034 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 1649 5.01 %random
Rwork0.2265 ---
obs0.2299 32911 89.02 %-
all-32911 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.497 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.1639 Å20 Å2-0 Å2
2--9.1639 Å20 Å2
3----18.3279 Å2
Refinement stepCycle: LAST / Resolution: 2.301→48.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 30 153 5013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084957
X-RAY DIFFRACTIONf_angle_d1.0546752
X-RAY DIFFRACTIONf_dihedral_angle_d14.9191753
X-RAY DIFFRACTIONf_chiral_restr0.066765
X-RAY DIFFRACTIONf_plane_restr0.005865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3005-2.36820.3432990.272100X-RAY DIFFRACTION74
2.3682-2.44470.3211270.26592509X-RAY DIFFRACTION87
2.4447-2.5320.3551580.24892624X-RAY DIFFRACTION92
2.532-2.63340.26161250.22942673X-RAY DIFFRACTION93
2.6334-2.75320.33431520.22522717X-RAY DIFFRACTION94
2.7532-2.89840.32971300.22512728X-RAY DIFFRACTION95
2.8984-3.080.29611440.22012754X-RAY DIFFRACTION95
3.08-3.31770.31111530.22412749X-RAY DIFFRACTION95
3.3177-3.65150.28511490.21482710X-RAY DIFFRACTION93
3.6515-4.17960.29061580.20312575X-RAY DIFFRACTION87
4.1796-5.26480.25721200.20492305X-RAY DIFFRACTION77
5.2648-48.04420.29761340.25522818X-RAY DIFFRACTION87

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