3TNX - JenaLib

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Title :   STRUCTURE OF THE PRECURSOR OF A THERMOSTABLE VARIANT OF PAPAIN AT 2.6 ANGSTROEM RESOLUTION

Authors :   S. Roy, D. Choudhury, J. K. Dattagupta, S. Biswas

Date :   02 Sep 11 (Deposition) - 12 Sep 12 (Release) - 28 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.62

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

Keywords :   Hydrolase, Cytoplasm For Recombinant Expression (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Roy, D. Choudhury, P. Aich, J. K. Dattagupta, S. Biswas
The Structure Of A Thermostable Mutant Of Pro-Papain Reveal Its Activation Mechanism
Acta Crystallogr. , Sect. D V. 68 1591 2012
PubMed-ID: 23151624 | Reference-DOI: 10.1107/S0907444912038607
(for further references see the PDB file header)

Molecule 1 - PAPAIN
	Chains	:	A, C
	EC Number	:	3.4.22.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30 EK/LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 27-345
	Mutation	:	YES
	Organism Common	:	MAMON
	Organism Scientific	:	CARICA PAPAYA
	Organism Taxid	:	3649
	Synonym	:	PAPAYA PROTEINASE I, PPI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:191 , THR A:192 , CYS A:260	BINDING SITE FOR RESIDUE CL A 320

Asymmetric Unit

No.	Residues
1	A:129	-	A:170
2	A:163	-	A:202
3	A:260	-	A:307
4	C:129	-	C:170
5	C:163	-	C:202
6	C:260	-	C:307

Asymmetric Unit

No.	Residues
1	Gly A:258	-	Pro A:259
2	Gly C:258	-	Pro C:259

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PAPA1_CARPA	152-163	2	A:126-137 C:126-137
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PAPA1_CARPA	290-300	2	A:264-274 C:264-274
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PAPA1_CARPA	303-322	2	A:277-296 C:277-296

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PAPA1_CARPA	152-163	1	A:126-137 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PAPA1_CARPA	290-300	1	A:264-274 -
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PAPA1_CARPA	303-322	1	A:277-296 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PAPA1_CARPA	152-163	1	- C:126-137
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PAPA1_CARPA	290-300	1	- C:264-274
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PAPA1_CARPA	303-322	1	- C:277-296

(no "Exon" information available for 3TNX)

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:310
 aligned with PAPA1_CARPA | P00784 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:310
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
          PAPA1_CARPA    36 NDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 345
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhh............................ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh.................hhhhhh.......eeeee...hhhhhhhhhh...eeeee...hhhhhheeeeee.........eeeeeeeee..eeeee...........eeeee.......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tnx A  10 NDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSAWAFSAVSTIESIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIRNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319

Chain C from PDB  Type:PROTEIN  Length:310
 aligned with PAPA1_CARPA | P00784 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:310
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
          PAPA1_CARPA    36 NDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 345
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhh............................ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh...hhhhh........hhhhhhh.......eeee....hhhhhhhhhh...eeeee...hhhhhheeeeee.........eeeeeeeee..eeeee...........eeeee.......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tnx C  10 NDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSAWAFSAVSTIESIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIRNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319

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 "SCOP Domain" information available for 3TNX)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (PAPA1_CARPA | P00784)

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:0097655	serpin family protein binding	Interacting selectively and non-covalently with any member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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	Sites
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	Cis Peptide Bonds
		Gly A:258 - Pro A:259	[ RasMol ]
		Gly C:258 - Pro C:259	[ RasMol ]

Biological Units
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	3tnx
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9pap	MATURE DOMAIN OF PAPAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (5, 5)

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