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(-) Description

Title :  SOLUTION STRUCTURE OF PEPTIDOGLYCAN ASSOCIATED LIPOPROTEIN FROM HAEMOPHILUS INFLUENZA BOUND TO UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMYL-MESO-2,6-DIAMINOPIMELOYL-D-ALANYL-D-ALANINE
 
Authors :  L. M. Parsons, F. Lin, J. Orban, Structure 2 Function Project (S2F)
Date :  01 Aug 05  (Deposition) - 14 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  P,U  (20x)
Keywords :  Alpha-Beta Sandwich, Structure 2 Function Project, S2F, Structural Genomics, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Parsons, F. Lin, J. Orban
Peptidoglycan Recognition By Pal, An Outer Membrane Lipoprotein.
Biochemistry V. 45 2122 2006
PubMed-ID: 16475801  |  Reference-DOI: 10.1021/BI052227I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN P6
    Chains: P
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PAL, OMPP6
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: OMP P6, 15 KDA PEPTIDOGLYCAN- ASSOCIATED LIPOPROTEIN, PC PROTEIN, PEPTIDOGLYCAN ASSOCIATED LIPOPROTEIN, PAL
 
Molecule 2 - UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMYL-MESO-2, 6-DIAMINOPIMELOYL-D-ALANYL-D-ALANINE
    Chains: U
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

NMR Structure (5, 6)
No.NameCountTypeFull Name
16CL1Mod. Amino Acid6-CARBOXYLYSINE
2AMU1Mod. Amino AcidBETA-N-ACETYLMURAMIC ACID
3DAL2Mod. Amino AcidD-ALANINE
4DGL1Mod. Amino AcidD-GLUTAMIC ACID
5UDP1Mod. Amino AcidURIDINE-5'-DIPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 2AIZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_2PS51123 OmpA-like domain profile.PAL_HAEIN40-153  1P:21-134
2OMPA_1PS01068 OmpA-like domain.PAL_HAEIN85-129  1P:66-110

(-) Exons   (0, 0)

(no "Exon" information available for 2AIZ)

(-) Sequences/Alignments

NMR Structure
   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 P from PDB  Type:PROTEIN  Length:134
 aligned with PAL_HAEIN | P10324 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:134
                                    29        39        49        59        69        79        89        99       109       119       129       139       149    
            PAL_HAEIN    20 CSSSNNDAAGNGAAQTFGGYSVADLQQRYNTVYFGFDKYDITGEYVQILDAHAAYLNATPAAKVLVEGNTDERGTPEYNIALGQRRADAVKGYLAGKGVDAGKLGTVSYGEEKPAVLGHDEAAYSKNRRAVLAY 153
               SCOP domains d2aizp1 P:1-134 Peptidoglycan-associated lipoprotein, PAL, periplasmic domain                                                          SCOP domains
               CATH domains -------------------------2aizP01 P:26-134 OmpA-like                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhh....eee........hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------OMPA_2  PDB: P:21-134 UniProt: 40-153                                                                              PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------OMPA_1  PDB: P:66-110 UniProt: 85-129        ------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aiz P   1 CSSSNNDAAGNGAAQTFGGYSVADLQQRYNTVYFGFDKYDITGEYVQILDAHAAYLNATPAAKVLVEGNTDERGTPEYNIALGQRRADAVKGYLAGKGVDAGKLGTVSYGEEKPAVLGHDEAAYSKNRRAVLAY 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain U from PDB  Type:PROTEIN  Length:7
                                       
               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
                 2aiz U   1 xxAxkxx   7
                            || ||||
                            1-UDP||
                             2-AMU|
                               4-DGL
                                5-6CL
                                 6-DAL
                                  7-DAL
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AIZ)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain P   (PAL_HAEIN | P10324)
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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