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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

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN 1
	Chains	:	A, B, C, D
	Organism Common	:	CAMEL
	Organism Scientific	:	CAMELUS DROMEDARIUS
	Organism Taxid	:	9838
	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 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:317 , CYS B:6 , ALA B:133 , LEU B:134 , HOH B:212 , HOH B:363 , ARG D:31 , ARG D:138	BINDING SITE FOR RESIDUE NAG B 172
2	AC2	SOFTWARE	HIS 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:173	BINDING SITE FOR RESIDUE TLA D 172
3	AC3	SOFTWARE	PRO C:151 , THR C:152 , HIS D:37 , THR D:38 , ALA D:39 , TYR D:71 , HIS D:146 , TLA D:172	BINDING SITE FOR RESIDUE GOL D 173

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 3QS0)

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

(no "Exon" information available for 3QS0)

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 '\|'

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	d3qs0a_	A:
1b	d3qs0b_	B:
1c	d3qs0c_	C:
1d	d3qs0d_	D:

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

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_2-3qs0D01	D:22-158
1b	Amidase_2-3qs0D02	D:22-158
1c	Amidase_2-3qs0D03	D:22-158
1d	Amidase_2-3qs0D04	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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

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)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (9, 9)

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