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(-) Description

Title :  PEPTIDOGLYCAN RECOGNITION PROTEIN-LB
 
Authors :  M. -S. Kim, M. Byun, B. -H. Oh
Date :  31 May 03  (Deposition) - 18 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidoglycan-Recognition Protein-Lb Isoform 2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. -S. Kim, M. Byun, B. -H. Oh
Crystal Structure Of Peptidoglycan Recognition Protein Lb From Drosophila Melanogaster
Nat. Immunol. V. 4 787 2003
PubMed-ID: 12845326  |  Reference-DOI: 10.1038/NI952

(-) Compounds

Molecule 1 - CG14704 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: PEPTIDOGLYCAN RECOGNITION PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3TLA1Ligand/IonL(+)-TARTARIC ACID
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , HIS A:152 , CYS A:160 , GLU A:182BINDING SITE FOR RESIDUE ZN A1185
2AC2SOFTWARETRP A:73 , ASN A:74 , ARG A:92 , HOH A:2026 , HOH A:2057BINDING SITE FOR RESIDUE EDO A1186
3AC3SOFTWAREHIS A:43 , THR A:158 , GLU A:159 , GLU A:182BINDING SITE FOR RESIDUE EDO A1187
4AC4SOFTWAREALA A:99 , ASN A:105 , GLN A:154 , HIS A:177 , ILE A:178 , ASN A:179 , HOH A:2026 , HOH A:2042BINDING SITE FOR RESIDUE TLA A1188

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:50 -A:56

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Mse A:46 -Pro A:47
2Cys A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OHT)

(-) 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:174
 aligned with PGPLB_DROME | Q8INK6 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:174
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    
          PGPLB_DROME    29 TARLLSRSDWGARLPKSVEHFQGPAPYVIIHHSYMPAVCYSTPDCMKSMRDMQDFHQLERGWNDIGYSFGIGGDGMIYTGRGFNVIGAHAPKYNDKSVGIVLIGDWRTELPPKQMLDAAKNLIAFGVFKGYIDPAYKLLGHRQVRDTECPGGRLFAEISSWPHFTHINDTEGVS 202
               SCOP domains d1ohta_ A: Peptidoglycan recognition protein-lb (Cg14704)                                                                                                                      SCOP domains
               CATH domains 1ohtA00 A:12-185 Lysozyme                                                                                                                                                      CATH domains
               Pfam domains -------------------Amidase_2-1ohtA01 A:31-164                                                                                                            --------------------- Pfam domains
         Sec.struct. author .eeeee.........eeeeeee...eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh......eeeeee.eeeeeee..............eeeeeeeee.......hhhhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oht A  12 TARLLSRSDWGARLPKSVEHFQGPAPYVIIHHSYmPAVCYSTPDCmKSmRDmQDFHQLERGWNDIGYSFGIGGDGmIYTGRGFNVIGAHAPKYNDKSVGIVLIGDWRTELPPKQmLDAAKNLIAFGVFKGYIDPAYKLLGHRQVRDTECPGGRLFAEISSWPHFTHINDTEGVS 185
                                    21        31        41    |   51     |  61 |      71        81     |  91       101       111       121    |  131       141       151       161       171       181    
                                                             46-MSE     57-MSE |                      87-MSE                                126-MSE                                                       
                                                                           60-MSE                                                                                                                         
                                                                              63-MSE
   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: Amidase_2] (23)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGPLB_DROME | Q8INK6)
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:0004040    amidase activity    Catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0061060    negative regulation of peptidoglycan recognition protein signaling pathway    Any process that decreases the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway.
    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:0000270    peptidoglycan metabolic process    The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
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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