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(-) Description

Title :  STRUCTURE OF THE EXTRA-MEMBRANOUS DOMAIN OF THE SECRETIN HOFQ FROM ACTINOBACILLUS ACTINOMYCETEMCOMITANS
 
Authors :  M. Tarry, M. Jaaskelainen, H. Tuominen, R. Ihalin, M. Hogbom
Date :  21 Dec 10  (Deposition) - 27 Apr 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Secretin, Dna Uptake, Competence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tarry, M. Jaaskelainen, A. Paino, H. Tuominen, R. Ihalin, M. Hogbom
The Extra-Membranous Domains Of The Competence Protein Hofq Show Dna Binding, Flexibility And A Shared Fold With Type I Kh Domains.
J. Mol. Biol. V. 409 642 2011
PubMed-ID: 21530539  |  Reference-DOI: 10.1016/J.JMB.2011.04.034

(-) Compounds

Molecule 1 - PROTEIN TRANSPORT PROTEIN HOFQ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-195
    Organism Scientific: AGGREGATIBACTER ACTINOMYCETEMCOMITANS
    Organism Taxid: 714
    Strain: DS7
    Synonym: EMHOFQ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:85 , GLN A:86 , LEU A:87 , LYS B:85 , GLN B:86 , LEU B:87BINDING SITE FOR RESIDUE GOL B1192
2AC2SOFTWAREGLU A:175 , ARG A:177 , SER A:178 , ARG B:177BINDING SITE FOR RESIDUE GOL A1192
3AC3SOFTWARELEU A:49 , ALA A:50 , ARG A:79 , SER A:80 , LYS A:83BINDING SITE FOR RESIDUE FMT A1193

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y3M)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3M)

(-) 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:135
 aligned with C9R226_AGGAD | C9R226 from UniProtKB/TrEMBL  Length:469

    Alignment length:165
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186     
         C9R226_AGGAD    27 QNPVFSIRLKQAPLVPTLQQLALAHNTNLIIDDELQGTVSLQLENVDLDQLFRSVAKIKQLDLWQENGIYYFTKGDTNTKFAGKMEEPFPLSLPMAEEPAQLTTATIKLHFAKASEVMKSLTGGSGSLLSPNGSITFDDRSNLLLIQDEPRSVRNIKKLIKELDK 191
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhh......eeeee-----..eeeeee.hhhhhhhhhhhhhh...eeeeeeeeee.-------------------------...eeeeee....hhhhhhhhhhh..........eeeee....eeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y3m A  27 QNPVFSIRLKQAPLVPTLQQLALAHNTNLIID-----TVSLQLENVDLDQLFRSVAKIKQLDLWQENGIYYFTK-------------------------AQLNTATIKLHFAKASEVMKSLTGGSGSLLSPNGSITFDDRSNLLLIQDEPRSVRNIKKLIKELDK 191
                                    36        46        56 |     |66        76        86        96   |     -         -       126       136       146       156       166       176       186     
                                                          58    64                                 100                       126                                                                 


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with C9R226_AGGAD | C9R226 from UniProtKB/TrEMBL  Length:469

    Alignment length:164
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
         C9R226_AGGAD    28 NPVFSIRLKQAPLVPTLQQLALAHNTNLIIDDELQGTVSLQLENVDLDQLFRSVAKIKQLDLWQENGIYYFTKGDTNTKFAGKMEEPFPLSLPMAEEPAQLTTATIKLHFAKASEVMKSLTGGSGSLLSPNGSITFDDRSNLLLIQDEPRSVRNIKKLIKELDK 191
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------Secretin_N-2y3mB01 B:130-191                                   Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------Secretin_N-2y3mB02 B:130-191                                   Pfam domains (2)
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhh...eeeeee.....eeeeeee.hhhhhhhhhhhhhhh..eeeeeeeeee.--------------------------..eeeeee....hhhhhhhhhhh..........eeeee....eeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y3m B  28 NPVFSIRLKQAPLVPTLQQLALAHNTNLIIDDELQGTVSLQLENVDLDQLFRSVAKIKQLDLWQENGIYYFTK--------------------------QLNTATIKLHFAKASEVMKSLTGGSGSLLSPNGSITFDDRSNLLLIQDEPRSVRNIKKLIKELDK 191
                                    37        47        57        67        77        87        97  |      -         -       127       137       147       157       167       177       187    
                                                                                                  100                        127
   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 2Y3M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3M)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (C9R226_AGGAD | C9R226)
biological process
    GO:0009297    pilus assembly    The assembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies. Pili are variously involved in transfer of nucleic acids, adherence to surfaces, and formation of pellicles. Is required for bacterial conjugation, or can play a role in adherence to surfaces (when it is called a fimbrium), and in the formation of pellicles.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.

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