3RNZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BACILLUS AMYLOLIQUEFACIENS PYROGLUTAMYL PEPTIDASE I

Authors :   Y. -C. Lo, A. H. -J. Wang

Date :   24 Apr 11 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. -C. Lo, W. -C. Su, T. -P. Ko, N. -C. Wang, A. H. -J. Wang
Terpyridine Platinum(Ii) Complexes Inhibit Cysteine Proteases By Binding To Active-Site Cysteine
J. Biomol. Struct. Dyn. V. 29 267 2011
PubMed-ID: 21875148

Molecule 1 - PYRROLIDONE-CARBOXYLATE PEPTIDASE
	Chains	:	A, B, C, D
	EC Number	:	3.4.19.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23(A)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PCP
	Mutation	:	YES
	Organism Scientific	:	BACILLUS AMYLOLIQUEFACIENS
	Organism Taxid	:	1390
	Strain	:	ATCC49763; RUB 500
	Synonym	:	5-OXOPROLYL-PEPTIDASE, PYROGLUTAMYL-PEPTIDASE I, PGP-I, PYRASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3RNZ)

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

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

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRASE_GLU	PS01333	Pyrrolidone-carboxylate peptidase glutamic acid active site.	PCP_BACAM	70-86	4	A:70-86 B:70-86 C:70-86 D:70-86
2	PYRASE_CYS	PS01334	Pyrrolidone-carboxylate peptidase cysteine active site.	PCP_BACAM	131-145	4	A:131-145 B:131-145 C:131-145 D:131-145

(no "Exon" information available for 3RNZ)

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:207
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
            PCP_BACAM     2 EKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIE 208
               SCOP domains d3rnza_ A: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......ee..eee..........................eee...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh........hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rnz A   2 EKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAMKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAAHEDDIE 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
            PCP_BACAM     1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIET 209
               SCOP domains d3rnzb_ B: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........hhhhhhhhhh...ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......ee..eee..........................eee...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh........hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ---------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rnz B   1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAMKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAAHEDDIET 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:PROTEIN  Length:206
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
            PCP_BACAM     2 EKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDI 207
               SCOP domains d3rnzc_ C: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........hhhhhhhhhh...ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......ee..eee..........................eee...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh........hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rnz C   2 EKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAMKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAAHEDDI 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain D from PDB  Type:PROTEIN  Length:206
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
            PCP_BACAM     2 EKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDI 207
               SCOP domains d3rnzd_ D: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........hhhhhhhhhh...ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee.......ee..eee..........................eee...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh........hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rnz D   2 EKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAMKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAAHEDDI 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

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 '\|'

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PCP_BACAM | P46107)

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.
	GO:0016920	pyroglutamyl-peptidase activity	Catalysis of the release of the N-terminal pyroglutamyl group from a peptide or protein.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rnz)

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	3rnz
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	3.4.19.3
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	PCP_BACAM \| P46107	:	1aug 3ro0

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (7, 7)

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