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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION CHAPERONE SYCD IN COMPLEX WITH A PEPTIDE OF THE TRANSLOCATOR YOPD
 
Authors :  M. Schreiner, H. H. Niemann
Date :  08 Mar 12  (Deposition) - 30 May 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Chaperone Binding Domain, Chaperone Peptide Complex, Pathogenictiy Factor, Translocator, Tetratricopeptide Repeat, Tpr, T3Ss, Virulence Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schreiner, H. H. Niemann
Crystal Structure Of The Yersinia Enterocolitica Type Iii Secretion Chaperone Sycd In Complex With A Peptide Of The Minor Translocator Yopd
Bmc Struct. Biol. V. 12 12 2012
PubMed-ID: 22708907  |  Reference-DOI: 10.1186/1472-6807-12-13

(-) Compounds

Molecule 1 - CHAPERONE SYCD
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS RIL
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 21-163
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630
    Other Details: YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703
    Strain: W22703
 
Molecule 2 - YOP EFFECTOR YOPD
    Chains: B
    Fragment: RESIDUES 56-65
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630
    Strain: W22703
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2BU35Ligand/Ion(R,R)-2,3-BUTANEDIOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:80 , HIS A:91BINDING SITE FOR RESIDUE SO4 A1160
2AC2SOFTWARELYS A:51 , TYR A:52 , GLU A:53 , ASP A:54BINDING SITE FOR RESIDUE BU3 A1161
3AC3SOFTWAREGLN A:85 , TYR A:86 , ASP A:87 , LEU A:88 , LYS A:117BINDING SITE FOR RESIDUE BU3 A1162
4AC4SOFTWAREGLU A:119 , LEU A:120 , ALA A:121 , GLU A:122BINDING SITE FOR RESIDUE BU3 A1163
5AC5SOFTWAREPRO A:107BINDING SITE FOR RESIDUE BU3 A1164
6AC6SOFTWAREILE B:61 , LYS B:62BINDING SITE FOR RESIDUE BU3 B1065

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AM9)

(-) Exons   (0, 0)

(no "Exon" information available for 4AM9)

(-) 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:131
 aligned with O87496_YEREN | O87496 from UniProtKB/TrEMBL  Length:168

    Alignment length:131
                                    38        48        58        68        78        88        98       108       118       128       138       148       158 
         O87496_YEREN    29 NEISSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIANKPEFKELSTRVSSMLEAIKLKKE 159
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4am9 A  29 NEISSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIANKPEFKELSTRVSSMLEAIKLKKE 159
                                    38        48        58        68        78        88        98       108       118       128       138       148       158 


Chain B from PDB  Type:PROTEIN  Length:10
 aligned with Q9R2G2_YEREN | Q9R2G2 from UniProtKB/TrEMBL  Length:306

    Alignment length:10
                                    64
         Q9R2G2_YEREN    55 SQVPELIKPS  64
               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
                 4am9 B  55 xQVPELIKPS  64
                            |       64
                           55-ACE     


Chain B from PDB  Type:PROTEIN  Length:10
 aligned with YOPD_YEREN | P37132 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:10
                                    64
           YOPD_YEREN    55 SQVPELIKPS  64
               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
                 4am9 B  55 xQVPELIKPS  64
                            |       64
                           55-ACE
   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  (0, 0)

(no "SCOP Domain" information available for 4AM9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AM9)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O87496_YEREN | O87496)
biological process
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

Chain B   (Q9R2G2_YEREN | Q9R2G2)

Chain B   (YOPD_YEREN | P37132)

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  Cis Peptide Bonds
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  4am9
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  O87496_YEREN | O87496
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  YOPD_YEREN | P37132
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 Related Entries

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

UniProtKB/TrEMBL
        O87496_YEREN | O87496: 2vgx 2vgy

(-) Related Entries Specified in the PDB File

2vgx STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION TRANSLOCATOR CHAPERONE SYCD
2vgy CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION TRANSLOCATOR CHAPERONE SYCD (ALTERNATIVE DIMER)