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Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL PEPTIDOGLYCAN-BINDING DOMAIN OF HUMAN PEPTIDOGLYCAN RECOGNITION PROTEIN IBETA

Authors :   S. Cho, R. A. Mariuzza

Date :   03 Feb 07 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Alpha/Beta Mix, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Cho, Q. Wang, C. P. Swaminathan, D. Hesek, M. Lee, G. J. Boons, S. Mobashery, R. A. Mariuzza
Structural Insights Into The Bactericidal Mechanism Of Huma Peptidoglycan Recognition Proteins
Proc. Natl. Acad. Sci. Usa V. 104 8761 2007
PubMed-ID: 17502600 | Reference-DOI: 10.1073/PNAS.0701453104

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN-I-BETA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PEPTIDOGLYCAN-BINDING DOMAIN
	Gene	:	PGRPIB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	NI	6	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:353 , HIS A:370 , HOH B:114 , ASP B:328 , GLN B:331	BINDING SITE FOR RESIDUE NI B 500
2	AC2	SOFTWARE	CYS A:210 , ASP A:328 , HIS B:370	BINDING SITE FOR RESIDUE NI A 501
3	AC3	SOFTWARE	HOH B:41 , ILE B:239 , HIS B:348 , SER B:356	BINDING SITE FOR RESIDUE NI B 502
4	AC4	SOFTWARE	ASN A:247 , GLU A:251 , HIS B:225	BINDING SITE FOR RESIDUE NI B 503
5	AC5	SOFTWARE	HIS A:373 , GLU B:324	BINDING SITE FOR RESIDUE NI A 504
6	AC6	SOFTWARE	GLU A:324 , PHE B:371 , HIS B:373	BINDING SITE FOR RESIDUE NI B 505

Asymmetric/Biological Unit

No.	Residues
1	A:210	-	A:332
2	A:226	-	A:270
3	A:246	-	A:252
4	B:210	-	B:332
5	B:226	-	B:270
6	B:246	-	B:252

Asymmetric/Biological Unit

No.	Residues
1	Leu A:231	-	Pro A:232
2	Ser A:356	-	Pro A:357
3	Leu B:231	-	Pro B:232
4	Ser B:356	-	Pro B:357

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031588	V	213	I	PGRP4_HUMAN	Polymorphism	12063091	A/B	I	213	I
2	UniProt	VAR_031589	D	301	N	PGRP4_HUMAN	Polymorphism	35347202	A/B	D	301	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000359650	1b	ENSE00001912151	chr1:153321022-153321004	19	PGRP4_HUMAN	-	0	0	-	-
1.2	ENST00000359650	2	ENSE00002157762	chr1:153320454-153320360	95	PGRP4_HUMAN	1-17	17	0	-	-
1.3	ENST00000359650	3	ENSE00001176998	chr1:153318667-153318578	90	PGRP4_HUMAN	17-47	31	0	-	-
1.4a	ENST00000359650	4a	ENSE00001409622	chr1:153317858-153317645	214	PGRP4_HUMAN	47-118	72	0	-	-
1.5	ENST00000359650	5	ENSE00001784702	chr1:153315684-153315566	119	PGRP4_HUMAN	118-158	41	0	-	-
1.6	ENST00000359650	6	ENSE00001072550	chr1:153314255-153314103	153	PGRP4_HUMAN	158-209	52	0	-	-
1.7	ENST00000359650	7	ENSE00001426683	chr1:153313055-153312857	199	PGRP4_HUMAN	209-275	67	2	A:210-275 B:210-275	66 66
1.8	ENST00000359650	8	ENSE00001202772	chr1:153309775-153309657	119	PGRP4_HUMAN	275-315	41	2	A:275-315 B:275-315	41 41
1.9	ENST00000359650	9	ENSE00001512647	chr1:153303421-153302596	826	PGRP4_HUMAN	315-373	59	2	A:315-373 B:315-373	59 59

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:164
 aligned with PGRP4_HUMAN | Q96LB8 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:164
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
          PGRP4_HUMAN   210 CPGVVPRSVWGARETHCPRMTLPAKYGIIIHTAGRTCNISDECRLLVRDIQSFYIDRLKSCDIGYNFLVGQDGAIYEGVGWNVQGSSTPGYDDIALGITFMGTFTGIPPNAAALEAAQDLIQCAMVKGYLTPNYLLVGHSDVARTLSPGQALYNIISTWPHFKH 373
               SCOP domains d2eava_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhh............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee.............hhh.eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---I---------------------------------------------------------------------------------------N------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:210-275 UniProt: 209-275 [INCOMPLETE]            ---------------------------------------Exon 1.9  PDB: A:315-373 UniProt: 315-373                   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.8  PDB: A:275-315 UniProt: 275-315---------------------------------------------------------- Transcript 1 (2)
                 2eav A 210 CPGIVPRSVWGARETHCPRMTLPAKYGIIIHTAGRTCNISDECRLLVRDIQSFYIDRLKSCDIGYNFLVGQDGAIYEGVGWNVQGSSTPGYDDIALGITFMGTFTGIPPNAAALEAAQDLIQCAMVKGYLTPNYLLVGHSDVARTLSPGQALYNIISTWPHFKH 373
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with PGRP4_HUMAN | Q96LB8 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:164
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
          PGRP4_HUMAN   210 CPGVVPRSVWGARETHCPRMTLPAKYGIIIHTAGRTCNISDECRLLVRDIQSFYIDRLKSCDIGYNFLVGQDGAIYEGVGWNVQGSSTPGYDDIALGITFMGTFTGIPPNAAALEAAQDLIQCAMVKGYLTPNYLLVGHSDVARTLSPGQALYNIISTWPHFKH 373
               SCOP domains d2eavb_ B: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eeee...eeee.................eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---I---------------------------------------------------------------------------------------N------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: B:210-275 UniProt: 209-275 [INCOMPLETE]            ---------------------------------------Exon 1.9  PDB: B:315-373 UniProt: 315-373                   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.8  PDB: B:275-315 UniProt: 275-315---------------------------------------------------------- Transcript 1 (2)
                 2eav B 210 CPGIVPRSVWGARETHCPRMTLPAKYGIIIHTAGRTCNISDECRLLVRDIQSFYIDRLKSCDIGYNFLVGQDGAIYEGVGWNVQGSSTPGYDDIALGITFMGTFTGIPPNAAALEAAQDLIQCAMVKGYLTPNYLLVGHSDVARTLSPGQALYNIISTWPHFKH 373
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369

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)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2eava_	A:
1b	d2eavb_	B:

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

(no "Pfam Domain" information available for 2EAV)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PGRP4_HUMAN | Q96LB8)

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:0016019	peptidoglycan receptor activity	Combining with a peptidoglycan and transmitting the signal to initiate a change in cell activity.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0016045	detection of bacterium	The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
	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:0002221	pattern recognition receptor signaling pathway	Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Ser A:356 - Pro A:357	[ RasMol ]
		Ser B:356 - Pro B:357	[ RasMol ]

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	2eav
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	PGRP4_HUMAN \| Q96LB8
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UniProtKB/Swiss-Prot
	PGRP4_HUMAN \| Q96LB8	:	2eax

2eax	THE SAME PROTEIN IN COMPLEX WITH GLYCOSAMYL MURAMYL PENTAPEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (0, 0)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (14, 14)

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Related Entries

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