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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL PROTEINASE) COMPLEXED WITH A FRAGMENT OF TYROSTATIN (THIS ENZYME RENAMED "SEDOLISIN" IN 2003)
 
Authors :  A. Wlodawer, M. Li, Z. Dauter, A. Gustchina, K. Uchida
Date :  29 Nov 00  (Deposition) - 13 Dec 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A,I
Keywords :  Serine-Carboxyl Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Wlodawer, M. Li, Z. Dauter, A. Gustchina, K. Uchida, H. Oyama, B. M. Dunn, K. Oda
Carboxyl Proteinase From Pseudomonas Defines A Novel Family Of Subtilisin-Like Enzymes.
Nat. Struct. Biol. V. 8 442 2001
PubMed-ID: 11323721  |  Reference-DOI: 10.1038/87610

(-) Compounds

Molecule 1 - SERINE-CARBOXYL PROTEINASE
    Chains: A
    EC Number: 3.4.23.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUKCP2212
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 306
    Synonym: PSCP, PSEUDOMONAPEPSIN, PEPSTATIN-INSENSITIVE CARBOXYL PROTEINASE
 
Molecule 2 - FRAGMENT OF TYROSTATIN
    Chains: I
    Engineered: YES
    Other Details: THE INHIBITOR WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
4UNK1Mod. Amino Acid

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:328 , VAL A:329 , GLY A:344 , GLY A:346 , ASP A:348 , HOH A:401BINDING SITE FOR RESIDUE CA A 374
2AC2SOFTWARELEU A:134 , GLY A:135 , SER A:167 , GLY A:169 , GLU A:171 , ARG A:179 , SER A:287 , HOH A:486BINDING SITE FOR RESIDUE ACT A 395
3AC3SOFTWARETHR A:24 , PRO A:196 , PRO A:244 , HOH A:417 , HOH A:461 , HOH A:480BINDING SITE FOR RESIDUE ACT A 396
4AC4SOFTWARELYS A:128 , GLY A:161 , SER A:307 , LEU A:308 , GLY A:309 , GOL A:392 , HOH A:635BINDING SITE FOR RESIDUE ACT A 397
5AC5SOFTWARESER A:324 , VAL A:326 , HIS A:327 , ASP A:357 , LYS A:360BINDING SITE FOR RESIDUE ACT A 398
6AC6SOFTWAREASN A:9 , PHE A:48 , ASN A:52 , THR A:186 , LEU A:273 , TYR A:275 , LEU A:280 , HOH A:434 , HOH A:489 , HOH A:515 , HOH A:564 , HOH A:866BINDING SITE FOR RESIDUE GOL A 391
7AC7SOFTWARESER A:20 , GLY A:309 , SER A:314 , PHE A:370 , ACT A:397 , HOH A:414 , HOH A:424 , HOH A:437 , HOH A:444 , HOH A:459 , HOH A:460BINDING SITE FOR RESIDUE GOL A 392
8AC8SOFTWAREASN A:125 , VAL A:126 , ASN A:306 , HOH A:465 , HOH A:484 , HOH A:680 , HOH A:751BINDING SITE FOR RESIDUE GOL A 393
9AC9SOFTWAREALA A:5 , ASN A:221 , GLU A:222 , HOH A:421 , HOH A:651BINDING SITE FOR RESIDUE GOL A 394

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:137 -A:176

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:191 -Pro A:192
2Leu A:259 -Pro A:260
3Tyr I:2 -Unk I:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GA6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEDOLISINPS51695 Sedolisin domain profile.PICP_PSESR219-583  1A:4-368

(-) Exons   (0, 0)

(no "Exon" information available for 1GA6)

(-) 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 A from PDB  Type:PROTEIN  Length:369
 aligned with PICP_PSESR | P42790 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:369
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576         
           PICP_PSESR   217 AGTAKGHNPTEFPTIYDASSAPTAANTTVGIITIGGVSQTLQDLQQFTSANGLASVNTQTIQTGSSNGDYSDDQQGQGEWDLDSQSIVGSAGGAVQQLLFYMADQSASGNTGLTQAFNQAVSDNVAKVINVSLGWCEADANADGTLQAEDRIFATAAAQGQTFSVSSGDEGVYECNNRGYPDGSTYSVSWPASSPNVIAVGGTTLYTTSAGAYSNETVWNEGLDSNGKLWATGGGYSVYESKPSWQSVVSGTPGRRLLPDISFDAAQGTGALIYNYGQLQQIGGTSLASPIFVGLWARLQSANSNSLGFPAASFYSAISSTPSLVHDVKSGNNGYGGYGYNAGTGWDYPTGWGSLDIAKLSAYIRSNGF 585
               SCOP domains d1ga6a_ A: Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ga6A00 A:2-370  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.......eeeeeeeeeee..hhhhhhhhhhhhhhh......eeeee..........hhhhhhhhhhhhhhhhhhh...eeeeeeeee......hhhhhhhhhhhhhhh...eeee...eehhhhhhhhhhhhhhhhhhhhhhh..eeeee......................ee.......eeeeeeeeee.....eeeeee.eeee.....eee...eeeeeee.hhhhhhh.....eeee..eeee.hhhhheeeee..eeeee.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...ee...........................eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SEDOLISIN  PDB: A:4-368 UniProt: 219-583                                                                                                                                                                                                                                                                                                                                     -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ga6 A   2 AGTAKGHNPTEFPTIYDASSAPTAANTTVGIITIGGVSQTLQDLQQFTSANGLASVNTQTIQTGSSNGDYSDDQQGQGEWDLDSQSIVGSAGGAVQQLLFYMADQSASGNTGLTQAFNQAVSDNVAKVINVSLGWCEADANADGTLQAEDRIFATAAAQGQTFSVSSGDEGVYECNNRGYPDGSTYSVSWPASSPNVIAVGGTTLYTTSAGAYSNETVWNEGLDSNGKLWATGGGYSVYESKPSWQSVVSGTPGRRLLPDISFDAAQGTGALIYNYGQLQQIGGTSLASPIFVGLWARLQSANSNSLGFPAASFYSAISSTPSLVHDVKSGNNGYGGYGYNAGTGWDYPTGWGSLDIAKLSAYIRSNGF 370
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361         


Chain I from PDB  Type:PROTEIN  Length:2
                                  
               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
                 1ga6 I   2 Yx   3
                             |
                             3-UNK
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GA6)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PICP_PSESR | P42790)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        PICP_PSESR | P42790: 1ga1 1ga4 1kdv 1kdy 1kdz 1ke1 1ke2 1nlu

(-) Related Entries Specified in the PDB File

1ga1 SAME PROTEIN WITH IODOTYROSTATIN FRAGMENT AT PH 7.5
1ga4 SAME PROTEIN WITH PSEUDOIODOTYROSTATIN AT PH 3.5