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- PDB-1nuf: Role of Calcium Ions in the Activation and Activity of the Transg... -

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Basic information

Entry
Database: PDB / ID: 1nuf
TitleRole of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme
ComponentsProtein-glutamine glutamyltransferase E
KeywordsTRANSFERASE / Transglutaminase 3 / metalloenzyme / calcium ion
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / extrinsic component of cytoplasmic side of plasma membrane / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / extrinsic component of cytoplasmic side of plasma membrane / protein modification process / calcium ion binding / structural molecule activity / protein-containing complex / extracellular exosome / cytoplasm
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
BROMIDE ION / Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAhvazi, B.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Roles of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme
Authors: Ahvazi, B. / Boeshans, K.M. / Idler, W. / Baxa, U. / Steinert, P.M.
#1: Journal: Embo J. / Year: 2002
Title: Three-dimensional structure of the human transglutaminase 3 enzyme:binding of calcium ions change structure for activation
Authors: Ahvazi, B. / Kim, H.C. / Kee, S.H. / Nemes, Z. / Steinert, P.M.
#2: Journal: J.Struct.Biol. / Year: 2001
Title: Crystallization and Preliminary X-ray Analysis of Human Transglutaminase 3 from Zymogen to Active Form
Authors: Kim, H.C. / Nemes, Z. / Idler, W.W. / Hyde, C.C. / Steinert, P.M. / Ahvazi, B.
History
DepositionJan 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_asym_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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 400COMPOUND THE ENZYME WAS PROTEOLYZED WITH DISPASE I FOR ACTIVATION AND MONO Q PURIFIED.
Remark 999SEQUENCE The following residues are noted as conflicts in the Swiss-Prot database: K562R, G654R ...SEQUENCE The following residues are noted as conflicts in the Swiss-Prot database: K562R, G654R (sequence database numbering). According to the author, residue 251 (sequence database numbering) is Asp and does not represent a mutation but a mistake in the Swiss-Prot database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutamine glutamyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,17210
Polymers76,6711
Non-polymers5029
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.74, 115.84, 61.96
Angle α, β, γ (deg.)90, 94.14, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein-glutamine glutamyltransferase E / TGase E / TGE / TGE / Transglutaminase 3


Mass: 76670.500 Da / Num. of mol.: 1 / Mutation: F264L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM3 / Plasmid: Bac-N_Blue, Invitrogen / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08188, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 4%-8% (w/v) Peg 6K or 20K, 100 mM Tris-HCl (pH 8.5) , VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
20.1 mMbeta-octylglucoside1drop
320 mMTris-HCl1droppH8.0
41 mMEDTA1drop
5125 mM1dropNaCl
64-8 %(w/v)PEG60001reservoiror PEG20000
7100 mMTris-HCl1reservoirpH8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X9B20.92
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEJun 7, 2000mirrors
ADSC QUANTUM 42CCDJun 7, 2000mirrors
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.921
ReflectionResolution: 2.7→20 Å / Num. obs: 22098 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 41.4 Å2 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→20 Å / % possible all: 91.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 199869
Reflection shell
*PLUS
Lowest resolution: 2.8 Å / % possible obs: 91.8 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1L9M

1l9m


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 2112 RANDOM
Rwork0.186 --
obs-21302 -
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--11.89 Å20 Å2-0.07 Å2
2---1.29 Å20 Å2
3---13.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 9 198 5473
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.334 315 -
Rwork0.266 --
obs-2981 9.6 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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