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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DROSOPHILA PATTERN-RECOGNITION RECEPTOR PGRP-SA
 
Authors :  C. -I. Chang, S. Pili-Floury, Y. Chelliah, B. Lemaitre, D. Mengin- Lecreulx, J. Deisenhofer
Date :  08 Jan 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mixed Beta-Sheet, Pi-Helix (One Turn), Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. -I. Chang, S. Pili-Floury, M. Herve, C. Parquet, Y. Chelliah, B. Lemaitre, D. Mengin-Lecreulx, J. Deisenhofer
A Drosophila Pattern Recognition Receptor Contains A Peptidoglycan Docking Groove And Unusual L, D-Carboxypeptidase Activity.
Plos Biol. V. 2 1293 2004
PubMed-ID: 15361936  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0020277
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN SA CG11709-PA
    ChainsA, B
    EC Number3.4.17.13
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineHI5
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorPFASTBAC
    Expression System Vector TypeBACULOVIRUS
    GenePGRP-SA
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , ASP A:144 , PO4 A:202 , ARG B:95 , GLY B:101 , TYR B:102 , ASN B:103 , ALA B:104 , HOH B:223BINDING SITE FOR RESIDUE PO4 B 201
2AC2SOFTWAREASP A:144 , PO4 A:203 , TYR B:100 , ASN B:103 , PO4 B:201BINDING SITE FOR RESIDUE PO4 A 202
3AC3SOFTWAREASP A:144 , TYR A:145 , HIS A:172 , PO4 A:202BINDING SITE FOR RESIDUE PO4 A 203
4AC4SOFTWAREASN A:176 , SER B:155 , THR B:156 , HOH B:224BINDING SITE FOR RESIDUE PO4 B 204
5AC5SOFTWAREGLY A:101 , TYR A:102 , ASN A:103 , ALA A:104BINDING SITE FOR RESIDUE PO4 A 205
6AC6SOFTWAREHIS A:178 , HOH A:246 , ASN B:176BINDING SITE FOR RESIDUE PO4 A 206

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:11 -A:134
2A:48 -A:54
3B:11 -B:134
4B:48 -B:54

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:33 -Pro A:34
2Ser A:158 -Pro A:159
3Ser B:158 -Pro B:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S2J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S2J)

(-) Exons   (0, 0)

(no "Exon" information available for 1S2J)

(-) Sequences/Alignments

Asymmetric 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:169
 aligned with PGPSA_DROME | Q9VYX7 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:169
                                                                                                                                                                                                203  
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196      |  
          PGPSA_DROME    37 CPTIKLKRQWGGKPSLGLHYQVRPIRYVVIHHTVTGECSGLLKCAEILQNMQAYHQNELDFNDISYNFLIGNDGIVYEGTGWGLRGAHTYGYNAIGTGIAFIGNFVDKLPSDAALQAAKDLLACGVQQGELSEDYALIAGSQVISTQSPGLTLYNEIQEWPHWLSNP--   -
               SCOP domains d1s2ja_ A: Peptidoglycan-recognition protein-SA (Cg11709)                                                                                                                 SCOP domains
               CATH domains 1s2jA00 A:11-179 Lysozyme                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.............eeeeeeee......hhhhhhhhhhhhhhhhhhhh.........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2j A  11 CPTIKLKRQWGGKPSLGLHYQVRPIRYVVIHHTVTGECSGLLKCAEILQNMQAYHQNELDFNDISYNFLIGNDGIVYEGTGWGLRGAHTYGYNAIGTGIAFIGNFVDKLPSDAALQAAKDLLACGVQQGELSEDYALIAGSQVISTQSPGLTLYNEIQEWPHWLSNPHH 179
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with PGPSA_DROME | Q9VYX7 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:168
                                                                                                                                                                                                203 
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196      | 
          PGPSA_DROME    37 CPTIKLKRQWGGKPSLGLHYQVRPIRYVVIHHTVTGECSGLLKCAEILQNMQAYHQNELDFNDISYNFLIGNDGIVYEGTGWGLRGAHTYGYNAIGTGIAFIGNFVDKLPSDAALQAAKDLLACGVQQGELSEDYALIAGSQVISTQSPGLTLYNEIQEWPHWLSNP-   -
               SCOP domains d1s2jb_ B: Peptidoglycan-recognition protein-SA (Cg11709)                                                                                                                SCOP domains
               CATH domains 1s2jB00 B:11-178 Lysozyme                                                                                                                                                CATH domains
           Pfam domains (1) ----------------Amidase_2-1s2jB01 B:27-162                                                                                                              ---------------- Pfam domains (1)
           Pfam domains (2) ----------------Amidase_2-1s2jB02 B:27-162                                                                                                              ---------------- Pfam domains (2)
         Sec.struct. author .....hhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s2j B  11 CPTIKLKRQWGGKPSLGLHYQVRPIRYVVIHHTVTGECSGLLKCAEILQNMQAYHQNELDFNDISYNFLIGNDGIVYEGTGWGLRGAHTYGYNAIGTGIAFIGNFVDKLPSDAALQAAKDLLACGVQQGELSEDYALIAGSQVISTQSPGLTLYNEIQEWPHWLSNPH 178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PGPSA_DROME | Q9VYX7)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0032500    muramyl dipeptide binding    Interacting selectively and non-covalently, in a non-covalent manner, with muramyl dipeptide; muramyl dipeptide is derived from peptidoglycan.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0016019    peptidoglycan receptor activity    Combining with a peptidoglycan and transmitting the signal to initiate a change in cell activity.
    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).
    GO:0008329    signaling pattern recognition receptor activity    Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species, or damage-associated molecular pattern (DAMP), an endogenous molecule released from damaged cells), and transmitting a signal to initiate a change in cell activity.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008063    Toll signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0016045    detection of bacterium    The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0002221    pattern recognition receptor signaling pathway    Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells.
    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:0006965    positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria    Any process that activates or increases the frequency, rate, or extent of biosynthesis of antibacterial peptides active against Gram-positive bacteria.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008592    regulation of Toll signaling pathway    Any process that modulates the frequency, rate or extent of the Tl signaling pathway.
    GO:0032494    response to peptidoglycan    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptidoglycan stimulus. Peptidoglycan is a bacterial cell wall macromolecule.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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.

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