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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE PEPTIDOGLYCAN HYDROLASE RIPB (RV1478) FROM MYCOBACTERIUM TUBERCULOSIS AT 1.6 RESOLUTION

Authors :   R. Schnell, D. Both, G. Schneider

Date :   20 Oct 10 (Deposition) - 31 Aug 11 (Release) - 19 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Peptidoglycan Hydrolase, Extracellular, Invasion Related Protein, Cell Wall, Nlpc-Like Module, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Both, G. Schneider, R. Schnell
Peptidoglycan Remodeling In Mycobacterium Tuberculosis: Comparison Of Structures And Catalytic Activities Of Ripa And Ripb.
J. Mol. Biol. V. 413 247 2011
PubMed-ID: 21864539 | Reference-DOI: 10.1016/J.JMB.2011.08.014

Molecule 1 - INVASION PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 30-241
	Gene	:	MT1525, RV1478
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	NLP/P60 FAMILY PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3PBI)

(no "Site" information available for 3PBI)

(no "SS Bond" information available for 3PBI)

(no "Cis Peptide Bond" information available for 3PBI)

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

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

(no "Exon" information available for 3PBI)

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
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Chain A from PDB  Type:PROTEIN  Length:199
 aligned with RIPB_MYCTO | P9WHU4 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:208
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        
           RIPB_MYCTO    34 GQWDPTLPALVSAGAPGDPLAVANASLQATAQATQTTLDLGRQFLGGLGINLGGPAASAPSAATTGASRIPRANARQAVEYVIRRAGSQMGVPYSWGGGSLQGPSKGVDSGANTVGFDCSGLVRYAFAGVGVLIPRFSGDQYNAGRHVPPAEAKRGDLIFYGPGGGQHVTLYLGNGQMLEASGSAGKVTVSPVRKAGMTPFVTRIIEY 241
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......---------.hhhhhhhhhhhhhhhhhhhhhhhh...............ee.hhhhh..ee.hhhhhhhhhhhh.......hhhhhh...eeehhhhh....eeeehhhhh.eeeeeee..eeeeee....eeeeee.........eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pbi A  34 GQWDPTLPALVSAGAPGDPLAVANASLQATAQATQTTLDLGRQFLGGLGINLGGP---------TGASRIPRANARQAVEYVIRRAGSQMGVPYSWGGGSLQGPSKGVDSGANTVGFDCSGLVRYAFAGVGVLIPRFSGDQYNAGRHVPPAEAKRGDLIFYGPGGGQHVTLYLGNGQMLEASGSAGKVTVSPVRKAGMTPFVTRIIEY 241
                                    43        53        63        73        83    |    -    |  103       113       123       133       143       153       163       173       183       193       203       213       223       233        
                                                                                 88        98

Chain A from PDB  Type:PROTEIN  Length:199
 aligned with RIPB_MYCTU | P9WHU5 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:208
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        
           RIPB_MYCTU    34 GQWDPTLPALVSAGAPGDPLAVANASLQATAQATQTTLDLGRQFLGGLGINLGGPAASAPSAATTGASRIPRANARQAVEYVIRRAGSQMGVPYSWGGGSLQGPSKGVDSGANTVGFDCSGLVRYAFAGVGVLIPRFSGDQYNAGRHVPPAEAKRGDLIFYGPGGGQHVTLYLGNGQMLEASGSAGKVTVSPVRKAGMTPFVTRIIEY 241
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......---------.hhhhhhhhhhhhhhhhhhhhhhhh...............ee.hhhhh..ee.hhhhhhhhhhhh.......hhhhhh...eeehhhhh....eeeehhhhh.eeeeeee..eeeeee....eeeeee.........eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pbi A  34 GQWDPTLPALVSAGAPGDPLAVANASLQATAQATQTTLDLGRQFLGGLGINLGGP---------TGASRIPRANARQAVEYVIRRAGSQMGVPYSWGGGSLQGPSKGVDSGANTVGFDCSGLVRYAFAGVGVLIPRFSGDQYNAGRHVPPAEAKRGDLIFYGPGGGQHVTLYLGNGQMLEASGSAGKVTVSPVRKAGMTPFVTRIIEY 241
                                    43        53        63        73        83    |    -    |  103       113       123       133       143       153       163       173       183       193       203       213       223       233        
                                                                                 88        98

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

(no "SCOP Domain" information available for 3PBI)

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

(no "Pfam Domain" information available for 3PBI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RIPB_MYCTO | P9WHU4)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A (RIPB_MYCTU | P9WHU5)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

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