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(-) Description

Title :  STRUCTURE OF THE OPCA ADHESION FROM NEISSERIA MENINGITIDIS DETERMINED BY CRYSTALLIZATION FROM THE CUBIC MESOPHASE
 
Authors :  V. Cherezov, W. Liu, J. P. Derrick, B. Luan, A. Aksimentiev, V. Katritch, M. Caffrey
Date :  05 Oct 07  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Invasin, Adhesin, Beta Barrel, Outer Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Cherezov, W. Liu, J. P. Derrick, B. Luan, A. Aksimentiev, V. Katritch, M. Caffrey
In Meso Crystal Structure And Docking Simulations Suggest An Alternative Proteoglycan Binding Site In The Opca Outer Membrane Adhesin.
Proteins V. 71 24 2008
PubMed-ID: 18076035  |  Reference-DOI: 10.1002/PROT.21841
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487
    Synonym: OPCA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1OCT1Ligand/IonN-OCTANE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:207 , ILE A:251BINDING SITE FOR RESIDUE OCT A1254
2AC2SOFTWAREASN A:47 , GLN A:100 , THR A:101 , LYS A:120 , HOH A:2120BINDING SITE FOR RESIDUE SO4 A1255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VDF)

(-) 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:225
 aligned with Q9AE79_NEIME | Q9AE79 from UniProtKB/TrEMBL  Length:252

    Alignment length:247
                                                                                                                                                                                                                                                                               252 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246     | 
         Q9AE79_NEIME     7 ANEFTVHTDLSSISSTRAFLKEKHKAAKHISVRADIPFDANQGIRLEAGFGRSKKNIINLETDENKLGKTKNVKLPTGVPENRIDLYTGYTYTQTLSDSLNFRVGAGLGFESSKDSIKTTKHTLHSSRQSWLAKVHADLLSQLGNGWYINPWSEVKFDLNSRYKLNTGVTNLKKDINQKTNGWGFGLGANIGKKLGESASIEAGPFYKQRTYKESGEFSVTTKSGDVSLTIPKTSIREYGLRVGIK-   -
               SCOP domains d2vdfa_ A: Outer membrane adhesin/invasin OpcA                                                                                                                                                                                                          SCOP domains
               CATH domains 2vdfA00 A:7-253 OPCA outer membrane adhesin/invasin                                                                                                                                                                                                     CATH domains
               Pfam domains OpcA-2vdfA01 A:7-245                                                                                                                                                                                                                           -------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee..hhhhhh...........eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeee.------.eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee..-------.eeee..eeeeeeeeeeeee..--.eeeeeeeeeeeee.......-------.......eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vdf A   7 ANEFTVHTDLSSISSTRAFLKEKHKAAKHIGVRADIPFDANQGIRLEAGFGRSKKNIINLETDENKLGKTKNVKLPTGVPENRIDLYTGYTYTQTLSDSLNFRVGAGLGFESSKDSI------LHSSRQSWLAKVHADLLSQLGNGWYINPWSEVKFDLNSRYKLNT-------DINQKTNGWGFGLGANIGKKLG--ASIEAGPFYKQRTYKESGEFS-------VSLTIPKTSIREYGLRVGIKF 253
                                    16        26        36        46        56        66        76        86        96       106       116      |  -   |   136       146       156       166      |  -    |  186       196     | 206       216        |-      |236       246       
                                                                                                                                              123    130                                        173     181                  202  |                 225     233                    
                                                                                                                                                                                                                                205
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9AE79_NEIME | Q9AE79)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9AE79_NEIME | Q9AE79: 1k24

(-) Related Entries Specified in the PDB File

1k24 CRYSTAL STRUCTURE OF THE OPCA OUTER MEMBRANEADHESIN/INVASIN FROM NEISSERIA MENINGITIDIS
2j9s STRUCTURE OF THE OPCA ADHESION FROM NEISSERIA MENINGITIDIS DETERMINED BY CRYSTALLIZATION FROM THE CUBIC MESOPHASE