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Title :   STRUCTURAL CONSEQUENCES OF ACCOMMODATION OF FOUR NON-COGNATE AMINO-ACID RESIDUES IN THE S1 POCKET OF BOVINE TRYPSIN AND CHYMOTRYPSIN

Authors :   R. Helland, H. Czapinska, I. Leiros, M. Olufsen, J. Otlewski, A. O. Smalaas

Date :   15 Apr 03 (Deposition) - 20 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Trypsin; Chymotrypsin; Serine Proteinase; Bovine Pancreatic Trypsin Inhibitor; Protein-Protein Interaction; Non-Cognate Binding; S1 Pocket; Primary Specificity; Crystal Structure, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Helland, H. Czapinska, I. Leiros, M. Olufsen, J. Otlewski, A. O. Smalaas
Structural Consequences Of Accommodation Of Four Non-Cognate Amino Acid Residues In The S1 Pocket Of Bovine Trypsin And Chymotrypsin.
J. Mol. Biol. V. 333 845 2003
PubMed-ID: 14568540 | Reference-DOI: 10.1016/J.JMB.2003.08.059
(for further references see the PDB file header)

Molecule 1 - TRYPSINOGEN, CATIONIC
	Chains	:	A
	EC Number	:	3.4.21.4
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	BETA-TRYPSIN, FRAGMENT

Molecule 2 - PANCREATIC TRYPSIN INHIBITOR
	Chains	:	I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PAED4
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	T7 PROMOTER
	Synonym	:	BASIC PROTEASE INHIBITOR, BPI, BPTI, APROTININ

		1	2
Asymmetric/Biological Unit	:	A	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:1021 , HOH A:1044	BINDING SITE FOR RESIDUE CA A 600
2	AC2	SOFTWARE	GLU I:7 , ARG I:42 , HOH I:1069 , HOH I:1161 , HOH I:1168 , HOH I:1171 , HOH I:1180	BINDING SITE FOR RESIDUE SO4 I 601
3	AC3	SOFTWARE	ARG I:20 , TYR I:35 , GLY I:37 , ALA I:40 , HOH I:660 , HOH I:671 , HOH I:678 , HOH I:1134 , HOH I:1141 , HOH I:1164	BINDING SITE FOR RESIDUE SO4 I 602

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

No.	Residues
1	Arg I:1	-	Pro I:2

(no "SAP(SNP)/Variant" information available for 1P2I)

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.	TRY1_BOVIN	24-244	1	A: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.	TRY1_BOVIN	59-64	1	A: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.	TRY1_BOVIN	194-205	1	A: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	ENSBTAT00000033479	1	ENSBTAE00000401279	chr4:109299627-109299547	81	TRY1_BOVIN	1-16	16	0	-	-
1.2	ENSBTAT00000033479	2	ENSBTAE00000397626	chr4:109298170-109298011	160	TRY1_BOVIN	16-69	54	1	A:16-63 (gaps)	48
1.3	ENSBTAT00000033479	3	ENSBTAE00000409037	chr4:109297593-109297340	254	TRY1_BOVIN	69-154	86	1	A:63-151 (gaps)	89
1.4	ENSBTAT00000033479	4	ENSBTAE00000386782	chr4:109296654-109296518	137	TRY1_BOVIN	154-199	46	1	A:151-194	46
1.5	ENSBTAT00000033479	5	ENSBTAE00000422174	chr4:109295990-109295749	242	TRY1_BOVIN	200-248	49	1	A:195-245 (gaps)	52

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:223
 aligned with TRY1_BOVIN | P00760 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   
          TRY1_BOVIN     24 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  246
               SCOP domains d1p2ia_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1p2iA01     1p2iA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1p2iA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1p2iA02       CATH domains
               Pfam domains Trypsin-1p2iA01 A:16-238                                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.2  PDB: A:16-63 (gaps) UniProt: 16-69  ------------------------------------------------------------------------------------Exon 1.4  PDB: A:151-194 UniProt: 154-199     Exon 1.5  PDB: A:195-245 (gaps)                 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:63-151 (gaps) UniProt: 69-154                                        -------------------------------------------------------------------------------------------- Transcript 1 (2)
                1p2i A   16 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                             69                                                      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 d1p2ii_ I: Pancreatic trypsin inhibitor, BPTI              SCOP domains
               CATH domains 1p2iI00 I:1-58 Factor Xa Inhibitor                         CATH domains
               Pfam domains ---Kunitz_BPTI-1p2iI01 I:4-56                           -- Pfam domains
         Sec.struct. author ..hhhhh..........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
                1p2i I    1 RPDFCLEPPYTGPCGARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCLRTCGGA   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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Trypsin(ogen) (500)

Cow (Bos taurus) [TaxId: 9913] (392)

d1p2ia_

Class: Small proteins (3458)

Fold: BPTI-like (161)

Superfamily: BPTI-like (161)

Family: Small Kunitz-type inhibitors & BPTI-like toxins (128)

Protein domain: Pancreatic trypsin inhibitor, BPTI (85)

Cow (Bos taurus) [TaxId: 9913] (85)

d1p2ii_

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)

Cattle (Bos taurus) (61)

1p2iI00

I:1-58

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Cattle (Bos taurus) (308)

2a	1p2iA01	A:16-27,A:121-232
2b	1p2iA02	A:28-120,A:233-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Bos taurus (Bovine) (190)

Trypsin-1p2iA01

A:16-238

Clan: Protease_inhib (47)

Family: Kunitz_BPTI (45)

Bos taurus (Bovine) (33)

Kunitz_BPTI-1p2iI01

I:4-56

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRY1_BOVIN | P00760)

molecular function
	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: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.
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.
	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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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (9, 9)

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