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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   LACK OF THE TRANSITION STATE STABILIZATION SITE IS A FACTOR IN THE INACTIVITY OF TRYPSINOGEN, A SERINE PROTEASE ZYMOGEN. STRUCTURE OF DFP INHIBITED BOVINE TRYPSINOGEN AT 2.1 ANGSTROMS RESOLUTION

Authors :   M. O. Jones, R. M. Stroud

Date :   17 Mar 86 (Deposition) - 07 May 86 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase Zymogen (Serine Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. O. Jones, R. M. Stroud
Lack Of The Transition State Stabilization Site Is A Factor In The Inactivity Of Trypsinogen, A Serine Protease Zymogen. Structure Of Dfp Inhibited Bovine Trypsinogen At 2. 1 Angstroms Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRYPSINOGEN
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	DFP	1	Ligand/Ion	DIISOPROPYL PHOSPHONATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:263	BINDING SITE FOR RESIDUE CA A 247
2	AC2	SOFTWARE	PHE A:41 , HIS A:57 , GLY A:193 , ASP A:194 , SER A:195 , HOH A:254 , HOH A:257	BINDING SITE FOR RESIDUE DFP A 248
3	ACT	UNKNOWN	HIS A:57 , ASP A:102 , SER A:195	ACTIVE SITE
4	BIN	UNKNOWN	ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , GLY A:193 , ASP A:194 , SER A:214 , TRP A:215 , GLY A:216 , SER A:217 , GLY A:219 , CYS A:220	SPECIFIC BINDING POCKET
5	ION	UNKNOWN	GLU A:70 , ASP A:71 , ASN A:72 , ILE A:73 , ASN A:74 , VAL A:75 , VAL A:76 , GLU A:77 , GLY A:78 , ASN A:79 , GLU A:80	CALCIUM ION BINDING SITE

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

(no "Cis Peptide Bond" information available for 2TGD)

(no "SAP(SNP)/Variant" information available for 2TGD)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRY1_BOVIN	59-64	1	A:53-58
2	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:17-63 (gaps)	47
1.3	ENSBTAT00000033479	3	ENSBTAE00000409037	chr4:109297593-109297340	254	TRY1_BOVIN	69-154	86	1	A:63-151 (gaps)	90
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
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Chain A from PDB  Type:PROTEIN  Length:222
 aligned with TRY1_BOVIN | P00760 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:222
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
          TRY1_BOVIN     25 VGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  246
               SCOP domains d2tgda_ A: Trypsin(ogen)                                                                                                                                                                                                       SCOP domains
               CATH domains 2tgdA01    2tgdA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  2tgdA01 A:17-27,A:121-232 Trypsin-like serine proteases                                                     2tgdA02       CATH domains
               Pfam domains Trypsin-2tgdA01 A:17-238                                                                                                                                                                                               ------- Pfam domains
     Sec.struct. author (1) ...e....................eee......eeee.......eeeee............eeeee.eeeee............eeee..........................eeeee...............eeeeee..hhhhhhhhh......eeeee...............eeeee..eeeeeee...........----hhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee-------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:17-63 (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)
                2tgd A   17 VGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    26       |38        48        58       |69        79        89        99       109       119     ||130|      141       151       161       171       181   |   189       199    || 213   ||  223       233       243  
                                            34|                          65A||                                                     125|  ||                                                 184A 188A             204|     217|  |                        
                                             37                            66|                                                      127  ||                                                                        209      219  |                        
                                                                            69                                                         130|                                                                                   221A                        
                                                                                                                                        132

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)

d2tgda_

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)

Cattle (Bos taurus) (308)

1a	2tgdA01	A:17-27,A:121-232
1b	2tgdA02	A:28-120,A:233-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Bos taurus (Bovine) (190)

Trypsin-2tgdA01

A:17-238

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.

Asymmetric/Biological Unit
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	2tgd
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SS Bonds (6, 6)

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