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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LFW ECTODOMAIN OF THE PEPTIDOGLYCAN RECOGNITION PROTEIN LF
 
Authors :  N. Basbous, F. Coste, P. Leone, R. Vincentelli, J. Royet, C. Kellenberg A. Roussel
Date :  24 Nov 10  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immune System, Drosophila, Innate Immunity, Pgrp-Lf (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Basbous, F. Coste, P. Leone, R. Vincentelli, J. Royet, C. Kellenberger, A. Roussel
The Drosophila Peptidoglycan-Recognition Protein Lf Interacts With Peptidoglycan-Recognition Protein Lc To Downregulate The Imd Pathway.
Embo Rep. V. 12 327 2011
PubMed-ID: 21372849  |  Reference-DOI: 10.1038/EMBOR.2011.19

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN-RECOGNITION PROTEIN LF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: ORIGAMI
    Expression System Vector: PDEST14
    Expression System Vector Type: PLASMID
    Fragment: LFW ECTODOMAIN, RESIDUES 230-369
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: PGRP-LIKE PROTEIN, PGRP-LF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
3PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:241 , HOH A:2030 , TYR B:241 , HOH B:2020BINDING SITE FOR RESIDUE PG4 A1369
2AC2SOFTWAREHOH A:2106 , HOH A:2107BINDING SITE FOR RESIDUE PEG A1371
3AC3SOFTWARESER B:291BINDING SITE FOR RESIDUE NA B1368
4AC4SOFTWAREILE B:248 , ILE B:289 , GLY B:293 , TYR B:294BINDING SITE FOR RESIDUE PEG B1369

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:271 -A:277
2B:271 -B:277

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:256 -Pro A:257
2Pro A:321 -Pro A:322
3Leu B:256 -Pro B:257
4Pro B:321 -Pro B:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 2XZ8)

(-) 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 PGPLF_DROME | Q8SXQ7 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:135
                                   243       253       263       273       283       293       303       313       323       333       343       353       363     
          PGPLF_DROME   234 VKIVTRPYWLAQPPIVPLTPLKLPIESVRFVATNTPSCFTQAECTFRVRLLQNWHIESNGYKDINYNFVAAGDENIYEARGWDHSCEPPKDADELVVAFIGPSSSNKKIALELIKQGIKLGHISKNYSLIDDLEK 368
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhh..............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee...............eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xz8 A 234 VKIVTRPYWLAQPPIVPLTPLKLPIESVRFVATNTPSCFTQAECTFRVRLLQNWHIESNGYKDINYNFVAAGDENIYEARGWDHSCEPPKDADELVVAFIGPSSSNKKIALELIKQGIKLGHISKNYSLIDDLEK 368
                                   243       253       263       273       283       293       303       313       323       333       343       353       363     


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with PGPLF_DROME | Q8SXQ7 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:134
                                   243       253       263       273       283       293       303       313       323       333       343       353       363    
          PGPLF_DROME   234 VKIVTRPYWLAQPPIVPLTPLKLPIESVRFVATNTPSCFTQAECTFRVRLLQNWHIESNGYKDINYNFVAAGDENIYEARGWDHSCEPPKDADELVVAFIGPSSSNKKIALELIKQGIKLGHISKNYSLIDDLE 367
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhh..............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee...............eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xz8 B 234 VKIVTRPYWLAQPPIVPLTPLKLPIESVRFVATNTPSCFTQAECTFRVRLLQNWHIESNGYKDINYNFVAAGDENIYEARGWDHSCEPPKDADELVVAFIGPSSSNKKIALELIKQGIKLGHISKNYSLIDDLE 367
                                   243       253       263       273       283       293       303       313       323       333       343       353       363
   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  (0, 0)

(no "SCOP Domain" information available for 2XZ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XZ8)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PGPLF_DROME | Q8SXQ7)
molecular function
    GO:0008745    N-acetylmuramoyl-L-alanine amidase activity    Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
    GO:0042834    peptidoglycan binding    Interacting selectively and non-covalently, in a non-covalent manner, with peptidoglycan, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0098542    defense response to other organism    Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0046329    negative regulation of JNK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0061057    peptidoglycan recognition protein signaling pathway    A series of molecular signals initiated by binding of peptidoglycan to a receptor on the surface of the target cell and ending with regulation of a downstream cellular process. The main outcome of the Imd signaling is the production of antimicrobial peptides.
    GO:0009617    response to bacterium    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 stimulus from a bacterium.
cellular component
    GO:0031240    external side of cell outer membrane    The side of the outer membrane that is opposite to the side that faces the periplasm of the cell.
    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:0005887    integral component of plasma membrane    The component of the plasma 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

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UniProtKB/Swiss-Prot
        PGPLF_DROME | Q8SXQ7: 2f2l 2xz4

(-) Related Entries Specified in the PDB File

2xz4 CRYSTAL STRUCTURE OF THE LFZ ECTODOMAIN OF THE PEPTIDOGLYCAN RECOGNITION PROTEIN LF