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(-) Description

Title :  CRYSTAL STRUCTURE OF IPGC FROM SHIGELLA FLEXNERI
 
Authors :  M. Lunelli, R. K. Lokareddy, A. Zychlinsky, M. Kolbe
Date :  06 Apr 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Asymmetric Homodimer, Tetratricopeptide Repeat, Tpr, Chaperone, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lunelli, R. K. Lokareddy, A. Zychlinsky, M. Kolbe
Ipab-Ipgc Interaction Defines Binding Motif For Type Iii Secretion Translocator
Proc. Natl. Acad. Sci. Usa V. 106 9661 2009
PubMed-ID: 19478065  |  Reference-DOI: 10.1073/PNAS.0812900106

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN IPGC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-151
    Gene: IPGC
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: M90T

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:109 , GLN A:112 , LYS A:142 , HOH B:160BINDING SITE FOR RESIDUE SO4 A 152
2AC2SOFTWAREGLN A:85 , PHE A:86 , GLN A:87 , GLN A:88 , LEU A:117BINDING SITE FOR RESIDUE GOL A 153
3AC3SOFTWAREMET A:36 , ASP A:37 , TYR A:40 , ASN A:69 , ASP A:71 , TYR A:72BINDING SITE FOR RESIDUE GOL A 154
4AC4SOFTWAREASP A:33 , MET A:36 , ASP A:66 , ASN A:69 , TYR A:72BINDING SITE FOR RESIDUE GOL A 155
5AC5SOFTWAREPHE B:108 , HIS B:109 , GLN B:112 , LYS B:142 , HOH B:181BINDING SITE FOR RESIDUE SO4 B 152
6AC6SOFTWAREASN B:102 , ASP B:103 , TYR B:104 , SER B:134 , ASN B:135 , ASP B:136BINDING SITE FOR RESIDUE GOL B 153
7AC7SOFTWAREGLU B:137 , GLN B:144BINDING SITE FOR RESIDUE GOL B 154
8AC8SOFTWAREASP B:66 , TYR B:68 , ASN B:69BINDING SITE FOR RESIDUE GOL B 155
9AC9SOFTWAREASP B:37 , TYR B:40 , ASN B:69 , ASP B:71 , TYR B:72BINDING SITE FOR RESIDUE GOL B 156

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GYZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GYZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GYZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GYZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3GYZ)

(-) 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:143
 aligned with IPGC_SHIFL | P0A2U4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:143
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148   
           IPGC_SHIFL     9 ESISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gyz A   9 ESISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148   


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with IPGC_SHIFL | P0A2U4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:143
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148   
           IPGC_SHIFL     9 ESISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gyz B   9 ESISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3GYZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GYZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GYZ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IPGC_SHIFL | P0A2U4)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IPGC_SHIFL | P0A2U4: 3gz1 3gz2 3ks2

(-) Related Entries Specified in the PDB File

3gz1 IPGC IN COMPLEX WITH CHAPERONE BINDING REGION OF IPAB
3gz2 IPGC IN COMPLEX WITH AN IPAB PEPTIDE