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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDOGLYCAN RECOGNITION PROTEIN-LE IN COMPLEX WITH TRACHEAL CYTOTOXIN (MONOMERIC DIAMINOPIMELIC ACID-TYPE PEPTIDOGLYCAN)
 
Authors :  J. -H. Lim, M. -S. Kim, B. -H. Oh
Date :  29 Dec 05  (Deposition) - 26 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Pgrp, Tracheal Cytotoxin, Innate Immunity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -H. Lim, M. -S. Kim, H. -E. Kim, T. Yano, Y. Oshima, K. Aggarwal, W. E. Goldman, N. Silverman, S. Kurata, B. -H. Oh
Structural Basis For Preferential Recognition Of Diaminopimelic Acid-Type Peptidoglycan By A Subset Of Peptidoglycan Recognition Proteins
J. Biol. Chem. V. 281 8286 2006
PubMed-ID: 16428381  |  Reference-DOI: 10.1074/JBC.M513030200

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN-RECOGNITION PROTEIN-LE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 173-345
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Other Details: PEPTIDOGLYCAN RECOGNITION PROTEIN-LE IN COMPLEX WITH TRACHEAL CYTOTOXIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLD4Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MLD1Ligand/IonGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:206 , THR A:207 , HIS A:229 , ARG A:233 , TRP A:235 , ASN A:236 , TYR A:240 , ARG A:254 , ALA A:261 , HIS A:262 , LEU A:264 , ASN A:267 , HIS A:314 , ASN A:318 , THR A:320 , GLU A:321 , SER A:322 , HOH A:2027 , HOH A:2038 , HOH A:2040 , HOH A:2052 , HOH A:2054 , GLN B:186 , ARG B:223 , ASP B:224 , SER B:227 , GLU B:231 , ARG D:215BINDING SITE FOR RESIDUE MLD A1345
2AC2SOFTWAREHIS B:206 , THR B:207 , MET B:225 , HIS B:229 , ARG B:233 , TRP B:235 , ASN B:236 , TYR B:240 , ARG B:254 , ALA B:261 , HIS B:262 , ASN B:267 , ARG B:268 , HIS B:314 , ASN B:318 , THR B:320 , GLU B:321 , SER B:322 , HOH B:2026 , HOH B:2042 , HOH B:2059 , HOH B:2060 , HOH B:2062 , HOH B:2063 , ARG C:215 , ARG D:223 , SER D:227 , GLU D:231BINDING SITE FOR RESIDUE MLD B1344
3AC3SOFTWAREARG A:223 , ASP A:224 , SER A:227 , GLU A:231 , ARG B:215 , HIS C:206 , THR C:207 , HIS C:229 , ARG C:233 , TRP C:235 , ASN C:236 , TYR C:240 , ARG C:254 , ALA C:261 , HIS C:262 , LEU C:264 , ASN C:267 , HIS C:314 , ASN C:318 , THR C:320 , GLU C:321 , SER C:322 , HOH C:2023 , HOH C:2033 , HOH C:2036 , HOH C:2045 , HOH C:2048BINDING SITE FOR RESIDUE MLD C1344
4AC4SOFTWAREARG A:215 , ARG C:223 , ASP C:224 , SER C:227 , GLU C:231 , HIS D:206 , THR D:207 , HIS D:229 , ARG D:233 , TRP D:235 , ASN D:236 , TYR D:240 , ARG D:254 , ALA D:261 , HIS D:262 , LEU D:264 , ASN D:267 , HIS D:314 , ASN D:318 , THR D:320 , GLU D:321 , SER D:322 , HOH D:2017 , HOH D:2031 , HOH D:2033 , HOH D:2034 , HOH D:2035 , HOH D:2037BINDING SITE FOR RESIDUE MLD D1344
5AC5SOFTWAREGLU A:210 , SER A:211 , GLY A:277 , CYS A:278 , PHE A:279 , GLU A:282 , HOH B:2006BINDING SITE FOR RESIDUE GOL A1344

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CB3)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:197 -Pro A:198
2Ser A:322 -Pro A:323
3Leu B:197 -Pro B:198
4Ser B:322 -Pro B:323
5Leu C:197 -Pro C:198
6Ser C:322 -Pro C:323
7Leu D:197 -Pro D:198
8Ser D:322 -Pro D:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CB3)

(-) Exons   (0, 0)

(no "Exon" information available for 2CB3)

(-) 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:171
 aligned with PGPLE_DROME | Q9VXN9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:171
                                   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
          PGPLE_DROME   174 LSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQCFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
               SCOP domains d2cb3a1 A:174-344 Peptidoglycan-recognition protein-LE                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........eeeeeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee.eeeeee...............eeeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cb3 A 174 LSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQSFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
                                   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with PGPLE_DROME | Q9VXN9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:170
                                   184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344
          PGPLE_DROME   175 SAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQCFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
               SCOP domains d2cb3b_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..........eeeeeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee.eeeeee...............eeeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cb3 B 175 SAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQSFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
                                   184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344


Chain C from PDB  Type:PROTEIN  Length:174
 aligned with PGPLE_DROME | Q9VXN9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:174
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
          PGPLE_DROME   171 PKELSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQCFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
               SCOP domains d2cb3c_ C: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..........eeeeeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee.eeeeee...............eeeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cb3 C 171 GHELSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQSFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    


Chain D from PDB  Type:PROTEIN  Length:171
 aligned with PGPLE_DROME | Q9VXN9 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:171
                                   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
          PGPLE_DROME   174 LSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQCFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
               SCOP domains d2cb3d_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........eeeeeee...eeeeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee.eeeeee...............eeeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cb3 D 174 LSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIRDMQSFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGISFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESPGRRLYEEIQTWPHFYNIEEEE 344
                                   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CB3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CB3)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PGPLE_DROME | Q9VXN9)
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: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: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:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    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: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:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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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