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(-) Description

Title :  MAD STRUCTURE OF THE PERIPLASMIQUE DOMAIN OF THE ESCHERICHIA COLI PAL PROTEIN
 
Authors :  C. Abergel, A. Walburger, E. Bouveret, J. M. Claverie
Date :  20 Jan 03  (Deposition) - 13 Feb 04  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Periplasmic, Peptidoglycan Binding, Tol System, Outer Membrane, Signal, Lipoprotein, Complete Proteome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abergel, A. Walburger, S. Chenivesse , C. Lazdunski
Crystallization And Preliminary Crystallographic Study Of The Peptidoglycan-Associated Lipoprotein From Escherichia Coli.
Acta Crystallogr. , Sect. D V. 57 317 2001
PubMed-ID: 11173492

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Fragment: PERIPLASMIC DOMAIN, RESIDUES 65-137
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: PERIPLASMIC DOMAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:54 , ASP A:55 , ALA A:88 , ASP A:89 , TYR A:96 , ASN A:97 , LEU A:100 , ARG A:104 , ARG A:146BINDING SITE FOR RESIDUE SO4 A 410
2AC2SOFTWARETYR A:51 , SER A:143BINDING SITE FOR RESIDUE SO4 A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OAP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OAP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OAP)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_1PS01068 OmpA-like domain.PAL_ECO57105-149  1A:84-128
PAL_ECOLI105-149  1A:84-128
PAL_SHIFL105-149  1A:84-128

(-) Exons   (0, 0)

(no "Exon" information available for 1OAP)

(-) 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:108
 aligned with PAL_ECO57 | P0A913 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:108
                                    75        85        95       105       115       125       135       145       155       165        
            PAL_ECO57    66 QQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY 173
               SCOP domains d1oapa_ A: Peptidoglycan-associated lipoprotein, PAL, periplasmic domain                                     SCOP domains
               CATH domains 1oapA00 A:45-152 OmpA-like                                                                                   CATH domains
               Pfam domains ------OmpA-1oapA01 A:51-146                                                                           ------ Pfam domains
         Sec.struct. author ....eee........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee...........hhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------OMPA_1  PDB: A:84-128 UniProt: 105-149       ------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oap A  45 QQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY 152
                                    54        64        74        84        94       104       114       124       134       144        


Chain A from PDB  Type:PROTEIN  Length:108
 aligned with PAL_ECOLI | P0A912 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:108
                                    75        85        95       105       115       125       135       145       155       165        
            PAL_ECOLI    66 QQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY 173
               SCOP domains d1oapa_ A: Peptidoglycan-associated lipoprotein, PAL, periplasmic domain                                     SCOP domains
               CATH domains 1oapA00 A:45-152 OmpA-like                                                                                   CATH domains
               Pfam domains ------OmpA-1oapA01 A:51-146                                                                           ------ Pfam domains
         Sec.struct. author ....eee........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee...........hhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ---------------------------------------OMPA_1  PDB: A:84-128 UniProt: 105-149       ------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oap A  45 QQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY 152
                                    54        64        74        84        94       104       114       124       134       144        


Chain A from PDB  Type:PROTEIN  Length:108
 aligned with PAL_SHIFL | P0A914 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:108
                                    75        85        95       105       115       125       135       145       155       165        
            PAL_SHIFL    66 QQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY 173
               SCOP domains d1oapa_ A: Peptidoglycan-associated lipoprotein, PAL, periplasmic domain                                     SCOP domains
               CATH domains 1oapA00 A:45-152 OmpA-like                                                                                   CATH domains
               Pfam domains ------OmpA-1oapA01 A:51-146                                                                           ------ Pfam domains
         Sec.struct. author ....eee........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee...........hhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------OMPA_1  PDB: A:84-128 UniProt: 105-149       ------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oap A  45 QQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVY 152
                                    54        64        74        84        94       104       114       124       134       144
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: OmpA] (9)

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAL_ECOLI | P0A912)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
cellular component
    GO:0032153    cell division site    The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
    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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0031246    intrinsic component of periplasmic side of cell outer membrane    The component of the cell outer membrane consisting of the gene products that that penetrate the periplasmic side of the cell outer membrane only, either directly or via some covalently attached hydrophobic anchor.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (PAL_SHIFL | P0A914)
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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (PAL_ECO57 | P0A913)
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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

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        PAL_ECOLI | P0A912: 2hqs 2w8b

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