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Title :   CRYSTAL STRUCTURE OF BACILLUS AMYLOLIQUEFACIENS PYROGLUTAMYL PEPTIDASE I AND TERPYRIDINE PLATINUM(II)

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

Date :   25 Apr 11 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Hydrolase-Hydrolase Inhibitor Complex (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)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	TPT	5	Ligand/Ion	2,2':6',2''-TERPYRIDINE PLATINUM(II) CHLORIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:10 , PHE A:13 , ASN A:19 , THR A:45 , GLN A:71 , ALA A:139 , CYS A:144 , HIS A:168 , HOH A:245 , HOH A:284 , HOH A:910	BINDING SITE FOR RESIDUE TPT A 480
2	AC2	SOFTWARE	PHE B:10 , PHE B:13 , THR B:45 , GLN B:71 , ALA B:139 , CYS B:144 , HIS B:168 , HOH B:337 , HOH B:923	BINDING SITE FOR RESIDUE TPT B 481
3	AC3	SOFTWARE	PHE C:10 , PHE C:13 , THR C:45 , GLN C:71 , ALA C:139 , CYS C:144 , HIS C:168 , HOH C:730	BINDING SITE FOR RESIDUE TPT C 482
4	AC4	SOFTWARE	PHE D:10 , PHE D:13 , THR D:45 , GLN D:71 , ALA D:139 , PHE D:142 , CYS D:144 , HIS D:168 , HOH D:454 , HOH D:728	BINDING SITE FOR RESIDUE TPT D 483
5	AC5	SOFTWARE	HIS D:158 , HIS D:159 , PRO D:160 , HIS D:161 , HOH D:507 , HOH D:688	BINDING SITE FOR RESIDUE TPT D 484

(no "SS Bond" information available for 3RO0)

(no "Cis Peptide Bond" information available for 3RO0)

(no "SAP(SNP)/Variant" information available for 3RO0)

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 3RO0)

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 d3ro0a_ A: 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
                 3ro0 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 d3ro0b_ 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
                 3ro0 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:207
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
            PCP_BACAM     1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDI 207
               SCOP domains d3ro0c_ 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
                 3ro0 C   1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAMKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAAHEDDI 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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 d3ro0d_ 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
                 3ro0 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 3RO0)

(no "Pfam Domain" information available for 3RO0)

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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(no "Cis Peptide Bonds" information available for 3ro0)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

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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