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(-) Description

Title :  STRUCTURE OF THE PGRP-HD FROM ALVINELLA POMPEJANA
 
Authors :  V. Delfosse, N. Gagniere, E. Perrodou, O. Poch, O. Lecompte, C. Mayer
Date :  29 Sep 08  (Deposition) - 29 Sep 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pgrp-Hd, Alvinella Pompejana, Immune System, Thermophile, Model System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Delfosse, N. Gagniere, E. Perrodou, O. Poch, O. Lecompte, C. Mayer
Structure Of The Pgrp-Hd From Alvinella Pompejana
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PGRP-HD - PEPTIDOGLYCAN RECOGNITION PROTEIN HOMOLOGUE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHGW
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PGRP-HD
    Organism Scientific: ALVINELLA POMPEJANA
    Organism Taxid: 6376

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EP1)

(-) Sites  (0, 0)

(no "Site" information available for 3EP1)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:125 -A:131
2A:211 -B:211
3A:242 -A:246
4B:125 -B:131
5B:242 -B:246

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EP1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EP1)

(-) Exons   (0, 0)

(no "Exon" information available for 3EP1)

(-) 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:167
 aligned with D0VX04_9ANNE | D0VX04 from UniProtKB/TrEMBL  Length:176

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
         D0VX04_9ANNE     1 LADSIVPRQQWAAIEPRRQIKMNGRADEIFLWQTGPDTCSLMGLTADKCQGCLQDSSCTEQIVKALQDADFKEGNDDIKYNFLIDQDGVIYEGRGWGVVGQHTKGRDSHSIGVAVIGDFGKKEPSQALQDALSKLIICGQAAEELSSGARLRTTPAMSGQAFYDMLDRCDGLCL 174
               SCOP domains d3ep1a_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhh.............eeeeeeee.hhhhhh...-------.......hhhhhhhhhhhhhhhh........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ep1 A  74 LADSIVPRQQWAAIEPRRQIKMNGRADEIFLWQTGPDTCSLMG-------GCLQDSSCTEQIVKALQDADFKEGNDDIKYNFLIDQDGVIYEGRGWGVVGQHTKGRDSHSIGVAVIGDFGKKEPSQALQDALSKLIICGQAAEELSSGARLRTTPAMSGQAFYDMLDRCDGLCL 247
                                    83        93       103       113  |      -|      133       143       153       163       173       183       193       203       213       223       233       243    
                                                                    116     124                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with D0VX04_9ANNE | D0VX04 from UniProtKB/TrEMBL  Length:176

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
         D0VX04_9ANNE     1 LADSIVPRQQWAAIEPRRQIKMNGRADEIFLWQTGPDTCSLMGLTADKCQGCLQDSSCTEQIVKALQDADFKEGNDDIKYNFLIDQDGVIYEGRGWGVVGQHTKGRDSHSIGVAVIGDFGKKEPSQALQDALSKLIICGQAAEELSSGARLRTTPAMSGQAFYDMLDRCDGLCL 174
               SCOP domains d3ep1b_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........................eeeeeeee.......----------.......hhhhhhhhhhhhhhhh........eee.....eee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ep1 B  74 LADSIVPRQQWAAIEPRRQIKMNGRADEIFLWQTGPDTCS----------GCLQDSSCTEQIVKALQDADFKEGNDDIKYNFLIDQDGVIYEGRGWGVVGQHTKGRDSHSIGVAVIGDFGKKEPSQALQDALSKLIICGQAAEELSSGARLRTTPAMSGQAFYDMLDRCDGLCL 247
                                    83        93       103       113         -|      133       143       153       163       173       183       193       203       213       223       233       243    
                                                                 113        124
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EP1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0VX04_9ANNE | D0VX04)
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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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.

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