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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE X-RAY CRYSTAL STRUCTURE OF PYRROLIDONE-CARBOXYLATE PEPTIDASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS HORIKOSHII

Authors :   M. Sokabe, T. Kawamura, N. Sakai, M. Yao, N. Watanabe, I. Tanaka

Date :   28 Feb 02 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)

Keywords :   Hydrolase, Thiol Protease, Complete Proteome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sokabe, T. Kawamura, N. Sakai, M. Yao, N. Watanabe, I. Tanaka
The X-Ray Crystal Structure Of Pyrrolidone-Carboxylate Peptidase From Hyperthermophilic Archaea Pyrococcus Horikoshii
J. Struct. Funct. Genom. V. 2 145 2002
PubMed-ID: 12836705 | Reference-DOI: 10.1023/A:1021257701676
(for further references see the PDB file header)

Molecule 1 - PYRROLIDONE-CARBOXYLATE PEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.19.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B(+)
	Expression System Strain	:	BL21-CODNPLUS(DE3)-RIL-X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH0596
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1IU8)

(no "Site" information available for 1IU8)

(no "SS Bond" information available for 1IU8)

Asymmetric Unit

No.	Residues
1	Tyr A:155	-	Pro A:156
2	Tyr B:155	-	Pro B:156

(no "SAP(SNP)/Variant" information available for 1IU8)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRASE_GLU	PS01333	Pyrrolidone-carboxylate peptidase glutamic acid active site.	PCP_PYRHO	65-81	2	A:65-81 B:65-81
2	PYRASE_CYS	PS01334	Pyrrolidone-carboxylate peptidase cysteine active site.	PCP_PYRHO	126-140	2	A:126-140 B:126-140

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRASE_GLU	PS01333	Pyrrolidone-carboxylate peptidase glutamic acid active site.	PCP_PYRHO	65-81	2	A:65-81 B:65-81
2	PYRASE_CYS	PS01334	Pyrrolidone-carboxylate peptidase cysteine active site.	PCP_PYRHO	126-140	2	A:126-140 B:126-140

Biological Unit 2 (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_PYRHO	65-81	4	A:65-81 B:65-81
2	PYRASE_CYS	PS01334	Pyrrolidone-carboxylate peptidase cysteine active site.	PCP_PYRHO	126-140	4	A:126-140 B:126-140

(no "Exon" information available for 1IU8)

Asymmetric 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:206
 aligned with PCP_PYRHO | O58321 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
            PCP_PYRHO     1 MKILLTGFEPFGGDDKNPTMDIVEALSERIPEVVGEILPVSFKRAREKLLKVLDDVRPDITINLGLAPGRTHISVERVAVNMIDARIPDNDGEQPKDEPIVEGGPAAYFATIPTREIVEEMKKNGIPAVLSYTAGTYLCNFAMYLTLHTSATKGYPKIAGFIHVPYTPDQVLEKKNTPSMSLDLEIKGVEIAIRVAQSALHSSQLR 206
               SCOP domains d1iu8a_ A: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                       SCOP domains
               CATH domains 1iu8A00 A:1-206  [code=3.40.630.20, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhh..eeeeeee......eeee.eee..ee...........eee........eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu8 A   1 MKILLTGFEPFGGDDKNPTMDIVEALSERIPEVVGEILPVSFKRAREKLLKVLDDVRPDITINLGLAPGRTHISVERVAVNMIDARIPDNDGEQPKDEPIVEGGPAAYFATIPTREIVEEMKKNGIPAVLSYTAGTYLCNFAMYLTLHTSATKGYPKIAGFIHVPYTPDQVLEKKNTPSMSLDLEIKGVEIAIRVAQSALHSSQLR 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with PCP_PYRHO | O58321 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
            PCP_PYRHO     1 MKILLTGFEPFGGDDKNPTMDIVEALSERIPEVVGEILPVSFKRAREKLLKVLDDVRPDITINLGLAPGRTHISVERVAVNMIDARIPDNDGEQPKDEPIVEGGPAAYFATIPTREIVEEMKKNGIPAVLSYTAGTYLCNFAMYLTLHTSATKGYPKIAGFIHVPYTPDQVLEKKNTPSMSLDLEIKGVEIAIRVAQSALHSSQLR 206
               SCOP domains d1iu8b_ B: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                       SCOP domains
               CATH domains 1iu8B00 B:1-206  [code=3.40.630.20, no name defined]                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhh..eeeeeee......eeee.eee..ee...........eee........eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iu8 B   1 MKILLTGFEPFGGDDKNPTMDIVEALSERIPEVVGEILPVSFKRAREKLLKVLDDVRPDITINLGLAPGRTHISVERVAVNMIDARIPDNDGEQPKDEPIVEGGPAAYFATIPTREIVEEMKKNGIPAVLSYTAGTYLCNFAMYLTLHTSATKGYPKIAGFIHVPYTPDQVLEKKNTPSMSLDLEIKGVEIAIRVAQSALHSSQLR 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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)

Pyrococcus horikoshii. Organism_taxid: 53953. (1)

1a	1iu8A00	A:1-206
1b	1iu8B00	B:1-206

(no "Pfam Domain" information available for 1IU8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PCP_PYRHO | O58321)

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.

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	Cis Peptide Bonds
		Tyr A:155 - Pro A:156	[ RasMol ]
		Tyr B:155 - Pro B:156	[ RasMol ]

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