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(-) Description

Title :  TWO INTRAMOLECULAR ISOPEPTIDE BONDS ARE IDENTIFIED IN THE CRYSTAL STRUCTURE OF THE STREPTOCOCCUS GORDONII SSPB C-TERMINAL DOMAIN
 
Authors :  N. Forsgren, R. J. Lamont, K. Persson
Date :  26 Nov 09  (Deposition) - 16 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion, Cell Wall, Antigen I/Ii, Peptidoglycan-Anchor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Forsgren, R. J. Lamont, K. Persson
Two Intramolecular Isopeptide Bonds Are Identified In The Crystal Structure Of The Streptococcus Gordonii Sspb C-Terminal Domain.
J. Mol. Biol. V. 397 740 2010
PubMed-ID: 20138058  |  Reference-DOI: 10.1016/J.JMB.2010.01.065

(-) Compounds

Molecule 1 - AGGLUTININ RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-VECTOR
    Fragment: C-TERMINAL DOMAIN, RESIDUES 1061-1413
    Organism Scientific: STREPTOCOCCUS GORDONII
    Organism Taxid: 1302
    Strain: M5
    Synonym: SSP-5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:1133 , TYR A:1134 , GLU A:1136 , LYS A:1186 , ALA A:1188 , HOH A:2040BINDING SITE FOR RESIDUE CA A2414
2AC2SOFTWAREASP A:1308 , TYR A:1309 , GLN A:1311 , ASN A:1354 , GLY A:1355 , HOH A:2037 , HOH A:2118BINDING SITE FOR RESIDUE CA A2415
3AC3SOFTWARETYR A:1077 , ASP A:1110 , ASP A:1112 , GLN A:1113 , ASP A:1332 , HOH A:2005 , HOH A:2022BINDING SITE FOR RESIDUE CA A2416

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WZA)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:1076 -Tyr A:1077

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WZA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WZA)

(-) Exons   (0, 0)

(no "Exon" information available for 2WZA)

(-) 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:338
 aligned with SSP5_STRGN | P16952 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:338
                                  1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405        
          SSP5_STRGN   1076 NYIKPTKVNKNKEGLNIDGKEVLAGSTNYYELTWDLDQYKGDKSSKEAIQNGFYYVDDYPEEALDVRPDLVKVADEKGNQVSGVSVQQYDSLEAAPKKVQDLLKKANITVKGAFQLFSADNPEEFYKQYVATGTSLVITDPMTVKSEFGKTGGKYENKAYQIDFGNGYATEVVVNNVPKITPKKDVTVSLDPTSENLDGQTVQLYQTFNYRLIGGLIPQNHSEELEDYSFVDDYDQAGDQYTGNYKTFSSLNLTMKDGSVIKAGTDLTSQTTAETDATNGIVTVRFKEDFLQKISLDSPFQAETYLQMRRIAIGTFENTYVNTVNKVAYASNTVRTTT 1413
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..................eeeeeeee.hhhhh....hhhhhh..eeeeee.....eee.hhhheeee........eeeeee......hhhhhhhhhhh.......eeeeee.hhhhhhhhh......eeeeeeeee..hhhhhheeeeeeeeeee..eeee...eeeee.....eeeee...................eeeeeee..............eeeeee.....eeeeeeeeeee...ee.....ee.....hhh.eeeeee....eeeeeehhhhhh.........eeeeeeeee...eeeee..eeee..eeee...eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wza A 1076 NYIKPTKVNKNKEGLNIDGKEVLAGSTNYYELTWDLDQYKGDKSSKEAIQNGFYYVDDYPEEALDVRPDLVKVADEKGNQVSGVSVQQYDSLEAAPKKVQDLLKKANITVKGAFQLFSADNPEEFYKQYVATGTSLVITDPMTVKSEFGKTGGKYENKAYQIDFGNGYATEVVVNNVPKITPKKDVTVSLDPTSENLDGQTVQLYQTFNYRLIGGLIPQNHSEELEDYSFVDDYDQAGDQYTGNYKTFSSLNLTMKDGSVIKAGTDLTSQTTAETDATNGIVTVRFKEDFLQKISLDSPFQAETYLQMRRIAIGTFENTYVNTVNKVAYASNTVRTTT 1413
                                  1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405
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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  (0, 0)

(no "SCOP Domain" information available for 2WZA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WZA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WZA)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SSP5_STRGN | P16952)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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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    Asn A:1076 - Tyr A:1077   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SSP5_STRGN | P16952: 2wd6 2woy 2wqs

(-) Related Entries Specified in the PDB File

2wd6 CRYSTAL STRUCTURE OF THE VARIABLE DOMAIN OF THE STREPTOCOCCUS GORDONII SURFACE PROTEIN SSPB
2woy CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF STREPTOCOCCUS GORDONII SURFACE PROTEIN SSPB
2wqs CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF STREPTOCOCCUS GORDONII SURFACE PROTEIN SSPB