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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDOGLYCAN RECOGNITION PROTEIN (PGRP-S) WITH A BOUND N-ACETYLGLUCOSAMINE IN THE DIFFUSION CHANNEL AT 2.5 A RESOLUTION
 
Authors :  D. Dube, P. Sharma, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Date :  19 Feb 11  (Deposition) - 16 Mar 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Immune Response, Secreted, Antimicrobial, Pgrp, Antibiotic, Peptidoglycan Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Dube, P. Sharma, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Peptidoglycan Recognition Protein (Pgrp-S) With A Bound N-Acetylglucosamine In The Diffusion Channel At 2. 5 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN 1
    ChainsA, B, C, D
    Organism CommonCAMEL
    Organism ScientificCAMELUS DROMEDARIUS
    Organism Taxid9838
    SynonymPEPTIDOGLYCAN RECOGNITION PROTEIN SHORT, PGRP-S

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:317 , CYS B:6 , ALA B:133 , LEU B:134 , HOH B:212 , HOH B:363 , ARG D:31 , ARG D:138BINDING SITE FOR RESIDUE NAG B 172
2AC2SOFTWAREHIS C:37 , ALA C:39 , THR C:152 , LEU C:153 , SER C:154 , HIS D:37 , ALA D:39 , THR D:152 , LEU D:153 , SER D:154 , GOL D:173BINDING SITE FOR RESIDUE TLA D 172
3AC3SOFTWAREPRO C:151 , THR C:152 , HIS D:37 , THR D:38 , ALA D:39 , TYR D:71 , HIS D:146 , TLA D:172BINDING SITE FOR RESIDUE GOL D 173

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:130
2A:22 -A:67
3A:43 -A:49
4B:6 -B:130
5B:22 -B:67
6B:43 -B:49
7C:6 -C:130
8C:22 -C:67
9C:43 -C:49
10D:6 -D:130
11D:22 -D:67
12D:43 -D:49

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Arg A:28 -Pro A:29
2Ser A:154 -Pro A:155
3Arg B:28 -Pro B:29
4Ser B:154 -Pro B:155
5Arg C:28 -Pro C:29
6Ser C:154 -Pro C:155
7Arg D:28 -Pro D:29
8Ser D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QS0)

(-) Exons   (0, 0)

(no "Exon" information available for 3QS0)

(-) 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:171
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3qs0a_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee...................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhhh.eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qs0 A   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3qs0b_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..............hhh.eeeeee.........hhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhh......hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qs0 B   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

Chain C from PDB  Type:PROTEIN  Length:171
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3qs0c_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.hhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..............hhh.eeeeee.........hhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qs0 C   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

Chain D from PDB  Type:PROTEIN  Length:171
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3qs0d_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Amidase_2-3qs0D01 D:22-158                                                                                                               ------------- Pfam domains (1)
           Pfam domains (2) ---------------------Amidase_2-3qs0D02 D:22-158                                                                                                               ------------- Pfam domains (2)
           Pfam domains (3) ---------------------Amidase_2-3qs0D03 D:22-158                                                                                                               ------------- Pfam domains (3)
           Pfam domains (4) ---------------------Amidase_2-3qs0D04 D:22-158                                                                                                               ------------- Pfam domains (4)
         Sec.struct. author ........ee.hhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhh..........eee.....eee..............hhh.eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qs0 D   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QS0)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PGRP1_CAMDR | Q9GK12)
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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:0001818    negative regulation of cytokine production    Any process that stops, prevents, or reduces the rate of production of a cytokine.
    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.
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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PGRP1_CAMDR | Q9GK122r2k 2r90 2z9n 3c2x 3cg9 3cor 3cxa 3ng4 3nno 3nw3 3o4k 3ogx 3qj1 3qv4 3rt4 3t2v 3t39 3tru 3uil 3uml 3umq 3usx 4fnn 4gf9 4opp 4orv 4oug 4q8s 4q9e 5dwf 5e0a 5e0b 5xgy

(-) Related Entries Specified in the PDB File

3ng4