3RT4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURAL BASIS OF RECOGNITION OF PATHOGEN-ASSOCIATED MOLECULAR PATTERNS AND INHIBITION OF PROINFLAMMATORY CYTOKINES BY CAMEL PEPTIDOGLYCAN RECOGNITION PROTEIN

Authors :   P. Sharma, D. Dube, A. Singh, B. Mishra, N. Singh, M. Sinha, S. Dey, P. Kau D. K. Mitra, S. Sharma, T. P. Singh

Date :   03 May 11 (Deposition) - 15 Jun 11 (Release) - 15 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Immune Response, Secreted, Antimicrobial, Pgrp, Peptidoglycan Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Sharma, D. Dube, A. Singh, B. Mishra, N. Singh, M. Sinha, S. Dey, P. Kaur, D. K. Mitra, S. Sharma, T. P. Singh
Structural Basis Of Recognition Of Pathogen-Associated Molecular Patterns And Inhibition Of Proinflammatory Cytokines By Camel Peptidoglycan Recognition Protein.
J. Biol. Chem. V. 286 16208 2011
PubMed-ID: 21454594 | Reference-DOI: 10.1074/JBC.M111.228163

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN 1
	Chains	:	A, B, C, D
	Organism Common	:	CAMEL,DROMEDARIES,DROMEDARY,ONE-HUMPED CAMEL
	Organism Scientific	:	CAMELUS DROMEDARIUS
	Organism Taxid	:	9838
	Strain	:	CAMELUS DROMEDARIUS
	Synonym	:	PEPTIDOGLYCAN RECOGNITION PROTEIN SHORT, PGRP-S

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	LP5	1	Ligand/Ion	(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
2	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:170 , LEU C:64 , TRP C:66 , LYS C:90 , ALA C:92 , HIS C:93 , ALA C:94 , GLY C:95 , PRO C:96 , ASN C:99 , PRO C:100 , GLN C:150 , PRO C:151 , HOH C:178 , HOH C:208 , HOH C:421 , HIS D:93 , ALA D:94 , GLY D:95 , PRO D:96 , THR D:97 , TRP D:98 , ASN D:99 , LYS D:144 , ASP D:148 , VAL D:149 , GLN D:150 , PRO D:151 , HOH D:180	BINDING SITE FOR RESIDUE LP5 C 501
2	AC2	SOFTWARE	HIS C:37 , ALA C:39 , THR C:152 , LEU C:153 , SER C:154 , HOH C:257 , HOH C:287 , HOH C:399 , HOH C:631 , HIS D:37 , ALA D:39 , THR D:152 , LEU D:153 , SER D:154	BINDING SITE FOR RESIDUE TLA C 6748

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 3RT4)

(no "PROSITE Motif" information available for 3RT4)

(no "Exon" information available for 3RT4)

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 d3rt4a_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee...................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rt4 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 d3rt4b_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee...................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rt4 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 d3rt4c_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rt4 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 d3rt4d_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Amidase_2-3rt4D01 D:22-158                                                                                                               ------------- Pfam domains (1)
           Pfam domains (2) ---------------------Amidase_2-3rt4D02 D:22-158                                                                                                               ------------- Pfam domains (2)
           Pfam domains (3) ---------------------Amidase_2-3rt4D03 D:22-158                                                                                                               ------------- Pfam domains (3)
           Pfam domains (4) ---------------------Amidase_2-3rt4D04 D:22-158                                                                                                               ------------- Pfam domains (4)
         Sec.struct. author ........ee.hhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rt4 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: N-acetylmuramoyl-L-alanine amidase-like (59)

Superfamily: N-acetylmuramoyl-L-alanine amidase-like (59)

Family: N-acetylmuramoyl-L-alanine amidase-like (53)

Protein domain: automated matches (30)

Camel (Camelus dromedarius) [TaxId: 9838] (27)

1a	d3rt4a_	A:
1b	d3rt4b_	B:
1c	d3rt4c_	C:
1d	d3rt4d_	D:

(no "CATH Domain" information available for 3RT4)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Amidase_2] (23)

Family: Amidase_2 (23)

Camelus dromedarius (Dromedary) (Arabian camel) (12)

1a	Amidase_2-3rt4D01	D:22-158
1b	Amidase_2-3rt4D02	D:22-158
1c	Amidase_2-3rt4D03	D:22-158
1d	Amidase_2-3rt4D04	D:22-158

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:28 - Pro A:29	[ RasMol ]
		Arg B:28 - Pro B:29	[ RasMol ]
		Arg C:28 - Pro C:29	[ RasMol ]
		Arg D:28 - Pro D:29	[ RasMol ]
		Ser A:154 - Pro A:155	[ RasMol ]
		Ser B:154 - Pro B:155	[ RasMol ]
		Ser C:154 - Pro C:155	[ RasMol ]
		Ser D:154 - Pro D:155	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3RT4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (12, 12)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Pfam Domains (1, 4)

Gene Ontology (9, 9)

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