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Title :   CRYSTAL STRUCTURE OF PORCINE ALPHA TRYPSIN BOUND WITH AUTO CATALYTICALY PRODUCED NATIVE PEPTIDE AT 2.15 A RESOLUTION

Authors :   V. Pattabhi, B. Syed Ibrahim, N. Shamaladevi

Date :   27 Jun 03 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,B,P

Keywords :   Serine Protease, Hydrolase, Peptide Trypsin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Pattabhi, B. Syed Ibrahim, N. Shamaladevi
Trypsin Activity Reduced By An Autocatalytically Produced Nonapeptide
J. Biomol. Struct. Dyn. V. 21 737 2004
PubMed-ID: 15106996
(for further references see the PDB file header)

Molecule 1 - TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

Molecule 2 - TRYPSIN
	Chains	:	B
	EC Number	:	3.4.21.4
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

Molecule 3 - 9-MER PEPTIDE FROM TRYPSIN
	Chains	:	P
	EC Number	:	3.4.21.4
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Other Details	:	IT IS AN OLIGOPEPTIDE FRAGMENT FROM NATIVE TRYPSIN BY AUTO CATALYSIS OF TRYPSIN PRODUCED DURING PREPARATION OF TRYPSIN.

		1	2	3
Asymmetric/Biological Unit	:	A	B	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CA	1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:60 , ALA A:129 , ALA A:130 , ALA A:132 , HOH A:288 , VAL B:162 , LEU B:163 , SER B:164 , ASP B:165 , ASP P:8	BINDING SITE FOR RESIDUE ACT P 390
2	AC2	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:257	BINDING SITE FOR RESIDUE CA A 256

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	B:157
2	A:42	-	A:58
3	A:128	-	B:232
4	A:136	-	B:201
5	B:168	-	B:182
6	B:191	-	B:220

(no "Cis Peptide Bond" information available for 1UHB)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRYP_PIG_001 *	I	20	V	TRYP_PIG	---	---	A	I	27	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRYP_PIG	9-229	1	A:16-145
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRYP_PIG	44-49	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRYP_PIG	179-190	2	B:189-200 P:3-9

(no "Exon" information available for 1UHB)

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:125
 aligned with TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:125
                                    18        28        38        48        58        68        78        88        98       108       118       128     
            TRYP_PIG      9 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTK  133
               SCOP domains d1uhb.1 A:,B: Trypsin(ogen)                                                                                                   SCOP domains
               CATH domains 1uhbA00 A:16-145 Trypsin-like serine proteases                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeee....eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee..... Sec.struct. author
                 SAPs(SNPs) -----------V----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-145 UniProt: 9-229                                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                1uhb A   16 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTK  145
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140     
                                             34|                            67|                                                     125|  ||             
                                              37                             69                                                      127  ||             
                                                                                                                                        130|             
                                                                                                                                         132

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:98
                                   143       153       163       173       183       193       203       213       223        
            TRYP_PIG    134 SSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  231
               SCOP domains d1uhb.1 A:,B: Trypsin(ogen)                                                                        SCOP domains
               CATH domains 1uhbB00 B:146-245 Trypsin-like serine proteases                                                    CATH domains
           Pfam domains (1) Trypsin-1uhbB01 B:146-238                                                                  ------- Pfam domains (1)
           Pfam domains (2) Trypsin-1uhbB02 B:146-238                                                                  ------- Pfam domains (2)
         Sec.struct. author ..........eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: - UniProt: 9-229                                                              -- PROSITE (1)
                PROSITE (2) ---------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                1uhb B  146 SSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  245
                                   155       165       175       184   |   193       203||     217| |    227       237        
                                                               184A 188A              204|     217| |                         
                                                                                       209      219 |                         
                                                                                                 221A

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:9
            TRYP_PIG    177 GKDSCQGDS  185
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_D PROSITE (1)
                PROSITE (2) --TRYPSIN PROSITE (2)
                 Transcript --------- Transcript
                1uhb P    1 GKDSCQGDS    9

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)

Pig (Sus scrofa) [TaxId: 9823] (33)

d1uhb.1

A:,B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Pig (Sus scrofa) (115)

1a	1uhbA00	A:16-145
1b	1uhbB00	B:146-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Sus scrofa (Pig) (47)

1a	Trypsin-1uhbB01	B:146-238
1b	Trypsin-1uhbB02	B:146-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,P (TRYP_PIG | P00761)

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: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.

Asymmetric/Biological Unit
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	1uhb
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1qqu	CRYSTAL STRUCTURE AT 1.63 A RESOLUTION OF THE NATIVE FORM OF PORCINE BETA-TRYPSIN: REVEALING AN ACETATE ION BINDING SITE AND FUNCTIONAL WATER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (3, 4)

Exons (0, 0)

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SCOP Domains (1, 1)

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