2RKQ - JenaLib

Title :   CRYSTAL STRUCTURE OF DROSOPHILA PEPTIDOGLYCAN RECOGNITION PROTEIN SD (PGRP-SD)

Authors :   A. Roussel, J. Royet, P. Leone, C. Kellenberger

Date :   17 Oct 07 (Deposition) - 25 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Innate Immunity; Toll; Pattern Recognition; Pgrp; Drosophila, Glycoprotein, Immune Response, Secreted, , Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Leone, V. Bischoff, C. Kellenberger, C. Hetru, J. Royet, A. Roussel
Crystal Structure Of Drosophila Pgrp-Sd Suggests Binding To Dap-Type But Not Lysine-Type Peptidoglycan
Mol. Immunol. V. 45 2521 2008
PubMed-ID: 18304640 | Reference-DOI: 10.1016/J.MOLIMM.2008.01.015
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:169
 aligned with PGPSD_DROME | Q9VS97 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:169
                                                                                                                                                                                                 186 
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       | 
          PGPSD_DROME    19 EVPIVTRAEWNAKPPNGAIDSMETPLPRAVIAHTAGGACADDVTCSQHMQNLQNFQMSKQKFSDIGYHYLIGGNGKVYEGRSPSQRGAFAGPNNDGSLGIAFIGNFEERAPNKEALDAAKELLEQAVKQAQLVEGYKLLGHRQVSATKSPGEALYALIQQWPNWSEEM-   -
               SCOP domains d2rkqa_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------Amidase_2-2rkqA01 A:28-162                                                                                                             ---------------- Pfam domains
         Sec.struct. author ...ee.hhhhh..............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------V--------------------A-----R------------------------------------------------------------------------------------------------------------------F---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rkq A  11 EVPIVTRAEWNAKPPNGAIDSMVTPLPRAVIAHTAGGACADDVTCSQHMRNLQNFQMSKQKFSDIGYHYLIGGNGKVYEGRSPSQRGAFAGPNNDGSLGIAFIGNFEERAPNKEALDAAKELLEQAVKQAQLVEGYKLLGHRQVSATKSPGEALYALIQQWPNWSEEML 178
                                    20      | 29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
                                          26A

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, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PGPSD_DROME | Q9VS97)

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: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: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: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: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.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2rkq)

	Sites
(no "Sites" information available for 2rkq)

	Cis Peptide Bonds
		Ser A:158 - Pro A:159	[ RasMol ]
		Thr A:33 - Pro A:34	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2rkq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PGPSD_DROME \| Q9VS97
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PGPSD_DROME \| Q9VS97
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description