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(-) Description

Title :  CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVERSIBLY BOUND PHOSPHONATE ESTERS
 
Authors :  R. Bone, D. A. Agard
Date :  26 Oct 90  (Deposition) - 15 Jan 93  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  E,I,P
Keywords :  Serine Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Bone, N. S. Sampson, P. A. Bartlett, D. A. Agard
Crystal Structures Of Alpha-Lytic Protease Complexes With Irreversibly Bound Phosphonate Esters.
Biochemistry V. 30 2263 1991
PubMed-ID: 1998685  |  Reference-DOI: 10.1021/BI00222A032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-LYTIC PROTEASE
    Chains: E
    EC Number: 3.4.21.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: LAC
    Organism Scientific: LYSOBACTER ENZYMOGENES
    Organism Taxid: 69
 
Molecule 2 - PHOSPHONATE ESTER INHIBITOR A
    Chains: P
    Engineered: YES
 
Molecule 3 - PHOSPHONATE ESTER INHIBITOR B(TRANSITION STATE)
    Chains: I
    Engineered: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : EIP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BOC2Mod. Amino AcidTERT-BUTYL HYDROGEN CARBONATE
2LAC1Mod. Amino AcidLACTIC ACID
3PVA2Mod. Amino Acid1-AMINO-2-METHYL-PROPYLPHOSPHONIC ACID
4SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA E:15A , ASN E:15B , ARG E:230 , PRO E:233 , HOH E:266 , HOH E:277 , HOH E:292 , HOH E:367 , HOH E:381BINDING SITE FOR RESIDUE SO4 E 1
2AC2SOFTWARESER E:40 , LEU E:41 , HIS E:57 , ARG E:125 , THR E:128 , TYR E:171 , GLY E:192A , ARG E:192B , GLY E:193 , ASP E:194 , SER E:195 , GLN E:208 , SER E:214 , GLY E:215 , GLY E:216 , VAL E:217A , GLY E:244 , HOH E:247 , HOH E:348 , PVA I:1 , PRO I:2 , ALA I:3 , ALA I:4 , BOC I:5 , HOH P:6 , HOH P:7 , HOH P:8 , HOH P:9 , HOH P:10 , HOH P:11BINDING SITE FOR CHAIN P OF PHOSPHONATE ESTER INHIBITOR A
3AC3SOFTWAREHIS E:57 , ARG E:125 , TYR E:171 , GLY E:192A , GLY E:193 , ASP E:194 , SER E:195 , SER E:214 , GLY E:215 , GLY E:216 , VAL E:217A , GLY E:244 , HOH E:348 , LAC P:-1 , ALA P:-2 , PVA P:1 , PRO P:2 , ALA P:3 , ALA P:4 , BOC P:5 , HOH P:6 , HOH P:8 , HOH P:10BINDING SITE FOR CHAIN I OF PHOSPHONATE ESTER INHIBITOR B(TRANSITION STATE)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1E:42 -E:58
2E:137 -E:159
3E:191 -E:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe E:94 -Pro E:99A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P11)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRLA_LYSEN231-236  1E:53-58
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRLA_LYSEN336-347  1E:191-200

(-) Exons   (0, 0)

(no "Exon" information available for 1P11)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain E from PDB  Type:PROTEIN  Length:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
          PRLA_LYSEN    200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  397
               SCOP domains d1p11e_ E: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains --1p11E01 E:16-115,E:231-242 Trypsin-like serine proteases                  1p11E02 E:116-230 Trypsin-like serine proteases                                                            1p11E01      -- CATH domains
               Pfam domains --Trypsin-1p11E01 E:16-226                                                                                                                                                         ------------------- Pfam domains
         Sec.struct. author .......eeee...eeee.........eeeeeehhhhh..........eeeeeeeeee.....eeeeee....eeeeeeee.................eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eee.....eeeeeeee...........hhhhh.eeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1p11 E  15A ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  244
                            ||   || 32  ||    45   |||| 51       |63  | ||  84      |99A       109       119 |||   126       136      |158       168   ||  179    ||192B       202||     215  |||||220 |||   227       236        
                            ||  19|    35|       48A|||         59| 65A ||         91|||                  120B||                    143|             172|       184|  ||        203|       217A|||| 221A||           235A         
                          15A|   29     39        48B||          62    67|          93||                   120C|                     156              174        190  ||         207        217B|||  221B|                        
                           15B                     48C|                 80           94|                    120D                                                   192A|                     217C||   221C                        
                                                    48D                              99A                                                                            192B                      217D|                               
                                                                                                                                                                                               217E                               


Chain I from PDB  Type:PROTEIN  Length:5
                                      
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                1p11 I    5 xAAPx    1
                            |||||
                            5-BOC
                             4|||
                              3||
                               2|
                                1-PVA


Chain P from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                1p11 P    5 xAAPxxA   -2
                            |||||||
                            |||||||
                            5-BOC||
                             4|||||
                              3||||
                               2|||
                                1-PVA
                                -1-LAC
                                 -2
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (PRLA_LYSEN | P00778)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1p11
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  PRLA_LYSEN | P00778
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  3.4.21.12
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PRLA_LYSEN | P00778: 1boq 1gba 1gbb 1gbc 1gbd 1gbe 1gbf 1gbh 1gbi 1gbj 1gbk 1gbl 1gbm 1p01 1p02 1p03 1p04 1p05 1p06 1p09 1p10 1p12 1qq4 1qrw 1qrx 1ssx 1tal 2alp 2h5c 2h5d 2lpr 2pro 2ull 3lpr 3m7t 3m7u 3pro 3qgj 3urc 3urd 3ure 4pro 5lpr 6lpr 7lpr 8lpr 9lpr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1P11)