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Title :   ANIONIC TRYPSIN VARIANT S195A IN COMPLEX WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) DETERMINED TO THE 1.46 A RESOLUTION LIMIT

Authors :   E. Zakharova, M. P. Horvath, D. P. Goldenberg, K. Curtice

Date :   04 Jan 09 (Deposition) - 17 Feb 09 (Release) - 18 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.46

Chains :   Asym./Biol. Unit : E,I

Keywords :   Enzyme-Inhibitor Complex, Peptide Bond Hydrolysis, Serine Protease, Calcium, Digestion, Hydrolase, Metal-Binding, Protease, Secreted, Zymogen, Pharmaceutical, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Zakharova, M. P. Horvath, D. P. Goldenberg
Structure Of A Serine Protease Poised To Resynthesize A Peptide Bond.
Proc. Natl. Acad. Sci. Usa V. 106 11034 2009
PubMed-ID: 19549826 | Reference-DOI: 10.1073/PNAS.0902463106
(for further references see the PDB file header)

Molecule 1 - ANIONIC TRYPSIN-2
	Chains	:	E
	EC Number	:	3.4.21.4
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PYT
	Expression System Strain	:	DLM101
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Gene	:	PRSS2, TRY2
	Mutation	:	YES
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	ANIONIC TRYPSIN II, PRETRYPSINOGEN II, SERINE PROTEASE 2

Molecule 2 - PANCREATIC TRYPSIN INHIBITOR
	Chains	:	I
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	BASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ

		1	2
Asymmetric/Biological Unit	:	E	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 12)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN E:34 , GLY E:38 , TYR E:39 , HIS E:40 , ARG E:67 , HOH E:770 , HOH E:817 , HOH E:882	BINDING SITE FOR RESIDUE EDO E 501
02	AC2	SOFTWARE	ILE E:47 , ASN E:48 , LEU E:123 , GLN E:239 , HOH E:755 , HOH E:841	BINDING SITE FOR RESIDUE EDO E 502
03	AC3	SOFTWARE	TYR E:59 , ILE E:88 , LYS E:90 , ASP E:236	BINDING SITE FOR RESIDUE EDO E 503
04	AC4	SOFTWARE	ASN E:143 , CYS E:191 , GLN E:192 , HOH E:763 , HOH E:919 , HOH E:923 , VAL I:34	BINDING SITE FOR RESIDUE EDO E 504
05	AC5	SOFTWARE	LYS E:97 , THR E:98 , LYS E:175 , TYR E:217 , HOH E:892 , HOH E:926 , ARG I:39	BINDING SITE FOR RESIDUE EDO E 505
06	AC6	SOFTWARE	GLY E:18 , PHE E:184A , GLU E:186 , GLY E:187 , GLY E:188 , LYS E:188A , HOH E:824	BINDING SITE FOR RESIDUE PG4 E 507
07	AC7	SOFTWARE	GLU E:70 , ASN E:72 , VAL E:75 , GLU E:77 , GLU E:80 , HOH E:759	BINDING SITE FOR RESIDUE CA E 601
08	AC8	SOFTWARE	LYS E:175 , HOH E:881 , HOH E:926 , ARG I:39 , ARG I:42 , HOH I:715	BINDING SITE FOR RESIDUE SO4 E 602
09	AC9	SOFTWARE	ASP I:3 , PHE I:4 , TYR I:10 , LYS I:41 , SO4 I:604	BINDING SITE FOR RESIDUE EDO I 506
10	BC1	SOFTWARE	HOH E:819 , ARG I:20 , TYR I:35 , ALA I:40 , HOH I:722 , HOH I:744 , HOH I:745 , HOH I:746 , HOH I:749	BINDING SITE FOR RESIDUE SO4 I 603
11	BC2	SOFTWARE	LYS I:41 , ARG I:42 , EDO I:506 , HOH I:705 , HOH I:707 , HOH I:741 , HOH I:756	BINDING SITE FOR RESIDUE SO4 I 604
12	BC3	SOFTWARE	HOH E:861 , ILE I:18 , ILE I:19 , ARG I:20 , LYS I:46 , HOH I:755 , HOH I:758 , HOH I:772	BINDING SITE FOR RESIDUE SO4 I 605

Asymmetric/Biological Unit

No.	Residues
1	E:22	-	E:157
2	E:42	-	E:58
3	E:128	-	E:232
4	E:136	-	E:201
5	E:168	-	E:182
6	E:191	-	E:220
7	I:5	-	I:55
8	I:14	-	I:38
9	I:30	-	I:51

(no "Cis Peptide Bond" information available for 3FP8)

(no "SAP(SNP)/Variant" information available for 3FP8)

Asymmetric/Biological Unit (5, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRY2_RAT	24-244	1	E:16-243
2	BPTI_KUNITZ_2	PS50279	Pancreatic trypsin inhibitor (Kunitz) family profile.	BPT1_BOVIN	40-90	1	I:5-55
3	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY2_RAT	59-64	1	E:53-58
4	BPTI_KUNITZ_1	PS00280	Pancreatic trypsin inhibitor (Kunitz) family signature.	BPT1_BOVIN	68-86	1	I:33-51
5	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRY2_RAT	194-205	1	E:189-200

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000018852	1	ENSRNOE00000331572	chr4:69088288-69088327	40	TRY2_RAT	1-14	14	0	-	-
1.2b	ENSRNOT00000018852	2b	ENSRNOE00000277233	chr4:69090744-69090903	160	TRY2_RAT	14-67	54	1	E:16-61 (gaps)	46
1.3	ENSRNOT00000018852	3	ENSRNOE00000105498	chr4:69092114-69092367	254	TRY2_RAT	67-152	86	1	E:61-149 (gaps)	89
1.4	ENSRNOT00000018852	4	ENSRNOE00000338303	chr4:69092772-69092908	137	TRY2_RAT	152-197	46	1	E:149-192	46
1.5	ENSRNOT00000018852	5	ENSRNOE00000134316	chr4:69093163-69093367	205	TRY2_RAT	198-246	49	1	E:193-245 (gaps)	54

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 E from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d3fp8e_ E: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 3fp8E01     3fp8E02 E:28-120,E:233-245 Trypsin-like serine proteases                                  3fp8E01 E:16-27,E:121-232 Trypsin-like serine proteases                                                     3fp8E02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: E:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.2b  PDB: E:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: E:149-192 UniProt: 152-197     Exon 1.5  PDB: E:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: E:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                3fp8 E   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDAGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57      ||68        78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                         64|                                                        125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                          66                                                         127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221A                        
                                                                                                                                         132

Chain I from PDB  Type:PROTEIN  Length:58
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:58
                                    45        55        65        75        85        
          BPT1_BOVIN     36 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA   93
               SCOP domains d3fp8i_ I: Pancreatic trypsin inhibitor, BPTI              SCOP domains
               CATH domains 3fp8I00 I:1-58 Factor Xa Inhibitor                         CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----BPTI_KUNITZ_2  PDB: I:5-55 UniProt: 40-90          --- PROSITE (2)
                PROSITE (3) --------------------------------BPTI_KUNITZ_1      ------- PROSITE (3)
                 Transcript ---------------------------------------------------------- Transcript
                3fp8 I    1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA   58
                                    10        20        30        40        50

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: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Factor Xa Inhibitor (116)

Homologous Superfamily: Factor Xa Inhibitor (116)

Brown rat,rat,rats (Rattus norvegicus) (2)

3fp8I00

I:1-58

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Brown rat,rat,rats (Rattus norvegicus) (3)

2a	3fp8E01	E:16-27,E:121-232
2b	3fp8E02	E:28-120,E:233-245

(no "Pfam Domain" information available for 3FP8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain E (TRY2_RAT | P00763)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0007584	response to nutrient	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Chain I (BPT1_BOVIN | P00974)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0019870	potassium channel inhibitor activity	Stops, prevents, or reduces the activity of a potassium channel.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0090331	negative regulation of platelet aggregation	Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0070495	negative regulation of thrombin-activated receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of thrombin-activated receptor protein signaling pathway activity. A thrombin receptor signaling pathway is the series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	3fp8
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3fp6	ANIONIC TRYPSIN IN COMPLEX WITH BPTI DETERMINED TO THE 1.49 A RESOLUTION LIMIT
3fp7	ANIONIC TRYPSIN VARIANT S195A IN COMPLEX WITH CLEAVED BPTI (LYS15/ALA16) DETERMINED TO THE 1.46 A RESOLUTION LIMIT
3tgi	ANIONIC TRYPSIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) DETERMINED TO THE 1.8 A RESOLUTION LIMIT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (5, 5)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (2, 3)

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Gene Ontology (21, 23)

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