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Asym./Biol. Unit (Jmol Viewer)

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Title :   PYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS

Authors :   M. R. Singleton, M. N. Isupov, J. A. Littlechild

Date :   13 Jan 98 (Deposition) - 15 Jul 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Peptidase, N-Pyroglutamate Hydrolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Singleton, M. Isupov, J. Littlechild
X-Ray Structure Of Pyrrolidone Carboxyl Peptidase From The Hyperthermophilic Archaeon Thermococcus Litoralis.
Structure Fold. Des. V. 7 237 1999
PubMed-ID: 10368293 | Reference-DOI: 10.1016/S0969-2126(99)80034-3
(for further references see the PDB file header)

Molecule 1 - PYRROLIDONE CARBOXYL PEPTIDASE
	Chains	:	A, B, C, D
	EC Number	:	3.4.19.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOSOL
	Expression System Gene	:	PCP
	Expression System Plasmid	:	PKK223-3
	Expression System Strain	:	MC1061
	Expression System Taxid	:	562
	Expression System Variant	:	JS5
	Expression System Vector Type	:	PLASMID
	Gene	:	PCP
	Organism Scientific	:	THERMOCOCCUS LITORALIS
	Organism Taxid	:	2265
	Other Details	:	CYS 143 OXIDIZED IN EACH SUBUNIT
	Other Details - Source	:	CAMR, PORTON DOWN, WILTSHIRE, UK
	Synonym	:	PYROGLUTAMYL AMINOPEPTIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:1 , TYR B:38	BINDING SITE FOR RESIDUE SO4 A 621
2	AC2	SOFTWARE	MET B:1 , LYS B:2 , ASN B:34	BINDING SITE FOR RESIDUE SO4 B 622
3	AC3	SOFTWARE	HOH B:691 , MET C:1 , HOH C:761 , SO4 D:624	BINDING SITE FOR RESIDUE SO4 C 623
4	AC4	SOFTWARE	MET C:1 , SO4 C:623 , HOH C:761 , MET D:1 , LYS D:2 , ASN D:34	BINDING SITE FOR RESIDUE SO4 D 624
5	AVE	UNKNOWN	GLU A:80 , CYS A:143 , HIS A:167	CATALYTIC TRIAD.

Asymmetric/Biological Unit

No.	Residues
1	A:190	-	C:190
2	B:190	-	D:190

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:159	-	Pro A:160
2	Tyr B:159	-	Pro B:160
3	Tyr C:159	-	Pro C:160
4	Tyr D:159	-	Pro D:160

(no "SAP(SNP)/Variant" information available for 1A2Z)

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_THELN	69-85	4	A:69-85 B:69-85 C:69-85 D:69-85
2	PYRASE_CYS	PS01334	Pyrrolidone-carboxylate peptidase cysteine active site.	PCP_THELN	130-144	4	A:130-144 B:130-144 C:130-144 D:130-144

(no "Exon" information available for 1A2Z)

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:220
 aligned with PCP_THELN | O07883 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            PCP_THELN     1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
               SCOP domains d1a2za_ A: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                                     SCOP domains
               CATH domains 1a2zA00 A:1-220  [code=3.40.630.20, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........hhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhh...eeeeeee......eeee.eee..........................eee....hhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eeeeeee...hhhh...............hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a2z A   1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with PCP_THELN | O07883 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            PCP_THELN     1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
               SCOP domains d1a2zb_ B: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                                     SCOP domains
               CATH domains 1a2zB00 B:1-220  [code=3.40.630.20, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........hhhhhhhhh..eee..eeeeeeee...hhhhhhhhhhhhhhh...eeeeeee......eeee.eee..........................eee....hhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh....eeeeeee...hhhh...............hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a2z B   1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:220
 aligned with PCP_THELN | O07883 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            PCP_THELN     1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
               SCOP domains d1a2zc_ C: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                                     SCOP domains
               CATH domains 1a2zC00 C:1-220  [code=3.40.630.20, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........hhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhh...eeeeeee......eeee.eee..........................eee....hhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eeeeeee...hhhh...............hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a2z C   1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain D from PDB  Type:PROTEIN  Length:220
 aligned with PCP_THELN | O07883 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            PCP_THELN     1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
               SCOP domains d1a2zd_ D: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                                     SCOP domains
               CATH domains 1a2zD00 D:1-220  [code=3.40.630.20, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........hhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhh...eeeeeee......eeee.eee..........................eee....hhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eeeeeee...hhhh...............hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a2z D   1 MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: [code=3.40.630.20, no name defined] (15)

Thermococcus litoralis. Organism_taxid: 2265. (1)

1a	1a2zA00	A:1-220
1b	1a2zB00	B:1-220
1c	1a2zC00	C:1-220
1d	1a2zD00	D:1-220

(no "Pfam Domain" information available for 1A2Z)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PCP_THELN | O07883)

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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		Tyr C:159 - Pro C:160	[ RasMol ]
		Tyr D:159 - Pro D:160	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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