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(-) Description

Title :  STRUCTURE OF THE STREPTOCOCCAL ENDOPEPTIDASE IDES, A NOVEL CYSTEINE PROTEINASE WITH STRICT SPECIFICITY FOR IGG
 
Authors :  K. Wenig, L. Chatwell, U. Von Pawel-Rammingen, L. Bjoerck, R. Huber, P. Sondermann
Date :  15 Nov 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Cysteine Proteinase, Papain-Like Fold With Major Insertions, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wenig, L. Chatwell, U. Von Pawel-Rammingen, L. Bjoerck, R. Huber, P. Sondermann
Structure Of The Streptococcal Endopeptidase Ides, A Cysteine Proteinase With Strict Specificity For Igg
Proc. Natl. Acad. Sci. Usa V. 101 17371 2004
PubMed-ID: 15574492  |  Reference-DOI: 10.1073/PNAS.0407965101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN SPY0861
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 49-339
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Synonym: IDES, IGG-DEGRADING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:84 , LEU A:92 , LEU A:93 , SER A:94 , ASN A:261 , HIS A:262 , HOH A:418 , HOH A:447 , HOH A:460 , HOH A:532BINDING SITE FOR RESIDUE SO4 A 1340

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y08)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y08)

(-) 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:286
 aligned with Q9F1R7_STRPY | Q9F1R7 from UniProtKB/TrEMBL  Length:339

    Alignment length:291
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338 
         Q9F1R7_STRPY    49 TSVWTKGVTPPANFTQGEDVFHAPYVANQGWYDITKTFNGKDDLLCGAATAGNMLHWWFDQNKDQIKRYLEEHPEKQKINFNGEQMFDVKEAIDTKNHQLDSKLFEYFKEKAFPYLSTKHLGVFPDHVIDMFINGYRLSLTNHGPTPVKEGSKDPRGGIFDAVFTRGDQSKLLTSRHDFKEKNLKEISDLIKKELTEGKALGLSHTYANVRINHVINLWGADFDSNGNLKAIYVTDSDSNASIGMKKYFVGVNSAGKVAISAKEIKEDNIGAQVLGLFTLSTGQDSWNQTN 339
               SCOP domains d1y08a_ A: IgG-specific endopeptidase IdeS (Sib38)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Mac-1-1y08A01 A:49-335                                                                                                                                                                                                                                                                         ---- Pfam domains
         Sec.struct. author ..ee..........ee....eee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeeeehhhhhhh......hhhhhhhhhh.....--.....hhhhhhhhhh..................................hhhhh.eeeee....hhhhhhhhhhhhhhh..eeeeee..---...eeeeeeeeee.....eeeeeee.........eeeeeeee.....eeee..........eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y08 A  49 TSVWTKGVTPPANFTQGEDVFHAPYVANQGWYDITKTFNGKDDLLSGAATAGNMLHWWFDQNKDQIKRYLEEHPEKQKINFNGEQMFDVKEAIDTKNHQLDSKLFEYFKEKAFPYL--KHLGVFPDHVIDMFINGYRLSLTNHGPTPVKEGSKDPRGGIFDAVFTRGDQSKLLTSRHDFKEKNLKEISDLIKKELTEGKALGLSHTY---RINHVINLWGADFDSNGNLKAIYVTDSDSNASIGMKKYFVGVNSAGKVAISAKEIKEDNIGAQVLGLFTLSTGQDSWNQTN 339
                                    58        68        78        88        98       108       118       128       138       148       158     | 168       178       188       198       208       218       228       238       248      |  -|      268       278       288       298       308       318       328       338 
                                                                                                                                             164  |                                                                                     255 259                                                                                
                                                                                                                                                167
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  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) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y08)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Mac-1] (1)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9F1R7_STRPY | Q9F1R7)
molecular function
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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