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- PDB-1p12: CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVER... -

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Basic information

Entry
Database: PDB / ID: 1p12
TitleCRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVERSIBLY BOUND PHOSPHONATE ESTERS
Components
  • ALPHA-LYTIC PROTEASEAlpha-lytic endopeptidase
  • PHOSPHONATE ESTER INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-(tert-butoxycarbonyl)-L-alanyl-L-alanyl-N-{(1R)-1-[(S)-[(1S)-2-{[(1R)-1-carboxyethyl]amino}-1-methyl-2-oxoethoxy](hyd roxy)phosphoryl]-2-methylpropyl}-L-prolinamide / Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBone, R. / Agard, D.A.
Citation
Journal: Biochemistry / Year: 1991
Title: Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate esters.
Authors: Bone, R. / Sampson, N.S. / Bartlett, P.A. / Agard, D.A.
#1: Journal: Biochemistry / Year: 1991
Title: Peptidic Phosphonylating Agents as Irreversible Inhibitors of Serine Proteases and Models of the Tetrahedral Intermediates
Authors: Sampson, N.S. / Bartlett, P.A.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure
Authors: Fujinaga, M. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
History
DepositionOct 26, 1990Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_chiral / struct_conn / struct_sheet / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_validate_chiral.auth_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_sheet.number_strands / _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: ALPHA-LYTIC PROTEASE
I: PHOSPHONATE ESTER INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6073
Polymers20,5112
Non-polymers961
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.790, 66.790, 79.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: PRO E 99A IS A CIS PROLINE. / 2: SEE REMARK 5. / 3: SEE REMARK 6.

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Components

#1: Protein ALPHA-LYTIC PROTEASE / Alpha-lytic endopeptidase


Mass: 19875.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Protein/peptide PHOSPHONATE ESTER INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 635.644 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-(tert-butoxycarbonyl)-L-alanyl-L-alanyl-N-{(1R)-1-[(S)-[(1S)-2-{[(1R)-1-carboxyethyl]amino}-1-methyl-2-oxoethoxy](hyd roxy)phosphoryl]-2-methylpropyl}-L-prolinamide
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PVA RESIDUE IN THE INHIBITOR IS THE ALPHA-AMINO PHOSPHONIC ACID ANALOG OF VAL IN WHICH THE C- ...THE PVA RESIDUE IN THE INHIBITOR IS THE ALPHA-AMINO PHOSPHONIC ACID ANALOG OF VAL IN WHICH THE C-TERMINAL CARBOXYL GROUP (COOH) HAS BEEN REPLACED WITH A PHOSPHONIC ACID GROUP (PO(OH)2). IN THE INHIBITOR, DESIGNATED CHAIN I, ESTER BONDS ARE FORMED FROM PHOSPHONATE PHOSPHOROUS OF THE OG OF SER E 195 AND TO O1 OF THE LAC I -1. INHIBITOR NUMBERING (CHAIN *I*, 5 TO -2) IS BY ANALOGY TO PROTEASE SUBSTRATE NOMENCLATURE IN WHICH THE RESIDUE PRIOR TO THE SCISSILE BOND IS THE *I* 1 RESIDUE, THE NEXT TOWARDS THE N-TERMINUS IS THE *I* 2 RESIDUE, ETC. RESIDUES TOWARDS THE C-TERMINUS ARE NUMBERED *I* -1 THEN *I* -2, ETC. (I. SCHECTER, A. BERGER, BIOCHEM. BIOPHYS. RES. COMMUN. 27, (1967) 157.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.3 Mlithium sulfate1drop
420 mg/mlprotein1drop
21dropLiOH
31dropH2SO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.124 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 5 183 1621
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.051

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