2XZ4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE LFZ ECTODOMAIN OF THE PEPTIDOGLYCAN RECOGNITION PROTEIN LF

Authors :   N. Basbous, F. Coste, P. Leone, R. Vincentelli, J. Royet, C. Kellenberg A. Roussel

Date :   23 Nov 10 (Deposition) - 13 Apr 11 (Release) - 13 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Immune System, Innate Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Basbous, F. Coste, P. Leone, R. Vincentelli, J. Royet, C. Kellenberger, A. Roussel
The Drosophila Peptidoglycan-Recognition Protein Lf Interacts With Peptidoglycan-Recognition Protein Lc To Downregulate The Imd Pathway.
Embo Rep. V. 12 327 2011
PubMed-ID: 21372849 | Reference-DOI: 10.1038/EMBOR.2011.19

Molecule 1 - PEPTIDOGLYCAN-RECOGNITION PROTEIN LF
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell Line	:	S2
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PMT/BIP/V5-HISA
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	LFZ ECTODOMAIN, RESIDUES 52-226
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	PGRP-LIKE PROTEIN, PGRP-LF

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	1PG	1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CU	1	Ligand/Ion	COPPER (II) ION
3	EDO	5	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	1PG	1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	1PG	-1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:59 , GLU A:64 , HOH A:2004	BINDING SITE FOR RESIDUE CU A 500
2	AC2	SOFTWARE	ASP A:61 , SER A:63 , TRP A:138 , HOH A:2114	BINDING SITE FOR RESIDUE EDO A 600
3	AC3	SOFTWARE	HIS A:87 , HIS A:88 , TYR A:122 , VAL A:145 , HIS A:196 , SER A:204 , HOH A:2115	BINDING SITE FOR RESIDUE EDO A 601
4	AC4	SOFTWARE	LYS A:175 , TYR A:191 , TRP A:216 , GLU B:172	BINDING SITE FOR RESIDUE 1PG A 650
5	AC5	SOFTWARE	ALA A:90 , GLU B:68 , LYS B:105 , GLN B:108 , ALA B:109 , HOH B:2112	BINDING SITE FOR RESIDUE EDO B 600
6	AC6	SOFTWARE	TYR B:102 , LYS B:105 , HOH B:2113	BINDING SITE FOR RESIDUE EDO B 601
7	AC7	SOFTWARE	HIS B:87 , HIS B:88 , TYR B:122 , HIS B:196	BINDING SITE FOR RESIDUE EDO B 602

Asymmetric Unit

No.	Residues
1	A:94	-	A:100
2	B:94	-	B:100

Asymmetric Unit

No.	Residues
1	Leu A:79	-	Pro A:80
2	Ser A:204	-	Pro A:205
3	Leu B:79	-	Pro B:80
4	Ser B:204	-	Pro B:205

(no "SAP(SNP)/Variant" information available for 2XZ4)

(no "PROSITE Motif" information available for 2XZ4)

(no "Exon" information available for 2XZ4)

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:165
 aligned with PGPLF_DROME | Q8SXQ7 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:165
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     
          PGPLF_DROME    58 HILDRSEWLGEPPSGKYPHLKLPVSNIIIHHTATEGCEQEDVCIYRMKTIQAFHMKSFGWVDIGYNFLVGGDGQIYVGRGWHIQGQHVNGYGAISVSIAFIGTFVNMEPPARQIEAAKRLMDEGVRLHRLQPDYHIYAHRQLSPTESPGQKLFELMQNWPRFTQD 222
               SCOP domains d2xz4a_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..................eeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xz4 A  58 HILDRSEWLGEPPSGKYPHLKLPVSNIIIHHTATEGCEQEDVCIYRMKTIQAFHMKSFGWVDIGYNFLVGGDGQIYVGRGWHIQGQHVNGYGAISVSIAFIGTFVNMEPPARQIEAAKRLMDEGVRLHRLQPDYHIYAHRQLSPTESPGQKLFELMQNWPRFTQD 222
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with PGPLF_DROME | Q8SXQ7 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:164
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217    
          PGPLF_DROME    58 HILDRSEWLGEPPSGKYPHLKLPVSNIIIHHTATEGCEQEDVCIYRMKTIQAFHMKSFGWVDIGYNFLVGGDGQIYVGRGWHIQGQHVNGYGAISVSIAFIGTFVNMEPPARQIEAAKRLMDEGVRLHRLQPDYHIYAHRQLSPTESPGQKLFELMQNWPRFTQ 221
               SCOP domains d2xz4b_ B: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------Amidase_2-2xz4B01 B:73-208                                                                                                              ------------- Pfam domains (1)
           Pfam domains (2) ---------------Amidase_2-2xz4B02 B:73-208                                                                                                              ------------- Pfam domains (2)
         Sec.struct. author .eehhhhhh..............eeeeeeee.......hhhhhhhhhhhhhhhhhhhh........eee.....eee..........---.....eeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xz4 B  58 HILDRSEWLGEPPSGKYPHLKLPVSNIIIHHTATEGCEQEDVCIYRMKTIQAFHMKSFGWVDIGYNFLVGGDGQIYVGRGWHIQGQH---YGAISVSIAFIGTFVNMEPPARQIEAAKRLMDEGVRLHRLQPDYHIYAHRQLSPTESPGQKLFELMQNWPRFTQ 221
                                    67        77        87        97       107       117       127       137      |  -|      157       167       177       187       197       207       217    
                                                                                                                144 148

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 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: automated matches (6)

Protein domain: automated matches (6)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (3)

1a	d2xz4a_	A:
1b	d2xz4b_	B:

(no "CATH Domain" information available for 2XZ4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Amidase_2 (23)

Drosophila melanogaster (Fruit fly) (5)

1a	Amidase_2-2xz4B01	B:73-208
1b	Amidase_2-2xz4B02	B:73-208

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGPLF_DROME | Q8SXQ7)

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:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	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:0098542	defense response to other organism	Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism.
	GO:0008340	determination of adult lifespan	The control of viability and duration in the adult phase of the life-cycle.
	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:0046329	negative regulation of JNK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	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:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
cellular component
	GO:0031240	external side of cell outer membrane	The side of the outer membrane that is opposite to the side that faces the periplasm of the cell.
	GO:0016021	integral component of membrane	The component of a 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.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Cis Peptide Bonds
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		Leu B:79 - Pro B:80	[ RasMol ]
		Ser A:204 - Pro A:205	[ RasMol ]
		Ser B:204 - Pro B:205	[ RasMol ]

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	PGPLF_DROME \| Q8SXQ7	:	2f2l 2xz8

2xz8	CRYSTAL STRUCTURE OF THE LFW ECTODOMAIN OF THE PEPTIDOGLYCAN RECOGNITION PROTEIN LF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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