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- PDB-1lnc: A STRUCTURAL ANALYSIS OF METAL SUBSTITUTIONS IN THERMOLYSIN -

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Basic information

Entry
Database: PDB / ID: 1lnc
TitleA STRUCTURAL ANALYSIS OF METAL SUBSTITUTIONS IN THERMOLYSIN
ComponentsTHERMOLYSIN
KeywordsHYDROLASE (METALLOPROTEASE)
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LYSINE / : / VALINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 1.8 Å
AuthorsHolland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 1995
Title: Structural analysis of zinc substitutions in the active site of thermolysin.
Authors: Holland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W.
#1: Journal: Biochemistry / Year: 1992
Title: Structural Comparison Suggests that Thermolysin and Related Neutral Proteases Undergo Hinge-Bending Motion During Catalysis
Authors: Holland, D.R. / Tronrud, D.E. / Pley, H.W. / Flaherty, K.M. / Stark, W. / Jansonius, J.N. / Mckay, D.B. / Matthews, B.W.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution
Authors: Holmes, M.A. / Matthews, B.W.
#3: Journal: Biochemistry / Year: 1982
Title: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans
Authors: Monzingo, A.F. / Matthews, B.W.
#4: Journal: Biochemistry / Year: 1981
Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis
Authors: Holmes, M.A. / Matthews, B.W.
#5: Journal: J.Biol.Chem. / Year: 1979
Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography
Authors: Bolognesi, M.C. / Matthews, B.W.
#6: Journal: J.Biol.Chem. / Year: 1977
Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin
Authors: Kester, W.R. / Matthews, B.W.
#7: Journal: J.Mol.Biol. / Year: 1977
Title: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates
Authors: Weaver, L.H. / Kester, W.R. / Matthews, B.W.
#8: Journal: Biochemistry / Year: 1977
Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis
Authors: Kester, W.R. / Matthews, B.W.
#9: Journal: Biochemistry / Year: 1976
Title: Role of Calcium in the Thermal Stability of Thermolysin
Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L.
#11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis
Authors: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A.
#12: Journal: J.Biol.Chem. / Year: 1974
Title: The Conformation of Thermolysin
Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R.
#13: Journal: Biochemistry / Year: 1974
Title: Binding of Lanthanide Ions to Thermolysin
Authors: Matthews, B.W. / Weaver, L.H.
#14: Journal: J.Mol.Biol. / Year: 1972
Title: The Structure of Thermolysin,an Electron Density Map at 2.3 Angstroms Resolution
Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W.
#15: Journal: Nature New Biol. / Year: 1972
Title: Amino-Acid Sequence of Thermolysin
Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H.
#16: Journal: Nature New Biol. / Year: 1972
Title: Three Dimensional Structure of Thermolysin
Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D.
#17: Journal: Nature New Biol. / Year: 1972
Title: Structure of Thermolysin
Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H.
#10: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1976
History
DepositionMay 13, 1994Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2012Group: Derived calculations
Revision 1.4Jul 18, 2012Group: Non-polymer description
Revision 1.5Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.6Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.7Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9509
Polymers34,3621
Non-polymers5878
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.900, 93.900, 131.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: CIS PROLINE - PRO E 51

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Components

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Protein , 1 types, 1 molecules E

#1: Protein THERMOLYSIN


Mass: 34362.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 178 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRESIDUES 1321 AND 1322 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS ...RESIDUES 1321 AND 1322 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS PRESUMED THAT THE ORIGIN OF THIS DIPEPTIDE IS THE C-TERMINAL TWO RESIDUES OF THE PROTEIN. SINCE THE C-TERMINUS APPEARS AT FULL OCCUPANCY, MOLECULES NOT INCORPORATED INTO THE CRYSTAL MUST HAVE BEEN SACRIFICED. A MANGANESE (MN 900) REPLACES THE NATIVE ZINC AND IS BOUND TO HOH 392, HOH 391, HIS 142, HIS 146, AND GLU 166. THIS METAL REPLACEMENT CAUSES GLU 143, MET 120 AND LEU TO ADOPT TWO DIFFERENT CONFORMATIONS. BOTH ARE MODELED. TWO NATIVE CALCIUMS (CA2, CA3) ARE ALSO REPLACED (BY MN 902 AND MN 903).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: unknown / Details: Holmes, M.A., (1982) J.Mol.Biol., 160, 623.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 M11CsCl
20.01 Mcalcium acetate12
30.01 MTris12
47 %dimethyl sulphoxide12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN / Detector: MULTIWIRE AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 94 % / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
TNTrefinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
XENGEN(HOWARDdata scaling
NIELSENdata scaling
XUONG)data scaling
RefinementMethod to determine structure: MOLECULAR SUBSTITUTION / Resolution: 1.8→20 Å / σ(F): 0 /
RfactorNum. reflection
obs0.152 30339
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 26 170 2628
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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