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(-) Description

Title :  RAT SUBMAXILLARY GLAND SERINE PROTEASE, TONIN. STRUCTURE SOLUTION AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION
 
Authors :  M. Fujinaga, M. N. G. James
Date :  03 Jun 87  (Deposition) - 16 Jan 88  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Hydrolase(Serine Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fujinaga, M. N. James
Rat Submaxillary Gland Serine Protease, Tonin. Structure Solution And Refinement At 1. 8 A Resolution.
J. Mol. Biol. V. 195 373 1987
PubMed-ID: 2821276  |  Reference-DOI: 10.1016/0022-2836(87)90658-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TONIN
    Chains: A
    Engineered: YES
    Organism Common: BLACK RAT
    Organism Scientific: RATTUS RATTUS
    Organism Taxid: 10117

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , HIS A:97 , HIS A:99 , GLU A:148BINDING SITE FOR RESIDUE ZN A 247

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:136 -A:201
4A:168 -A:182
5A:191 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK2_RAT25-256  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK2_RAT59-64  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK2_RAT205-216  1A:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK2_RAT25-256  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK2_RAT59-64  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK2_RAT205-216  1A:189-200
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK2_RAT25-256  2A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK2_RAT59-64  2A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK2_RAT205-216  2A:189-200

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000257011ENSRNOE00000267985chr1:94475840-9447575982KLK2_RAT1-16160--
1.2ENSRNOT000000257012ENSRNOE00000357170chr1:94473794-94473641154KLK2_RAT16-67521A:16-61 (gaps)46
1.3ENSRNOT000000257013ENSRNOE00000184072chr1:94472768-94472482287KLK2_RAT67-163971A:61-149 (gaps)101
1.4ENSRNOT000000257014ENSRNOE00000301192chr1:94472385-94472249137KLK2_RAT163-208461A:149-19246
1.5ENSRNOT000000257015ENSRNOE00000339422chr1:94471891-94471693199KLK2_RAT209-259511A:193-246 (gaps)55

(-) Sequences/Alignments

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
(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:228
 aligned with KLK2_RAT | P00759 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:235
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254     
            KLK2_RAT     25 IVGGYKCEKNSQPWQVAVINEYLCGGVLIDPSWVITAAHCYSNNYQVLLGRNNLFKDEPFAQRRLVRQSFRHPDYIPLIVTNDTEQPVHDHSNDLMLLHLSEPADITGGVKVIDLPTKEPKVGSTCLASGWGSTNPSEMVVSHDLQCVNIHLLSNEKCIETYKDNVTDVMLCAGEMEGGKDTCAGDSGGPLICDGVLQGITSGGATPCAKPKTPAIYAKLIKFTSWIKKVMKENP  259
               SCOP domains d1tona_ A: Tonin                                                                                                                                                                                                                            SCOP domains
               CATH domains 1tonA01     1tonA02 A:28-120,A:233-245 Trypsin-like serine proteases                                            1tonA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                      1tonA02      - CATH domains
               Pfam domains Trypsin-1tonA01 A:16-238                                                                                                                                                                                                           -------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeee..eeee.hhh.....eeee............eee.eeeeee........-------.........eeeee........................eeeeee...............eeeeeeee.hhhhhhhh...hhhheeeee...............eeee..eeeeee.............eeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 25-256                                                                                                                                                                                              --- PROSITE (1)
                PROSITE (2) ----------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-61 (gaps) [INCOMPLETE] -----------------------------------------------------------------------------------------------Exon 1.4  PDB: A:149-192 UniProt: 163-208     Exon 1.5  PDB: A:193-246 (gaps) UniProt: 209-259    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3  PDB: A:61-149 (gaps) UniProt: 67-163                                                   ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                1ton A   16 IVGGYKCEKNSQPWQVAVINEYLCGGVLIDPSWVITAAHCYSNNYQVLLGRNNLFKDEPFAQRRLVRQSFRHPDYIPLI-------PVHDHSNDLMLLHLSEPADITGGVKVIDLPTKEPKVGSTCLASGWGSTNPSEMVVSHDLQCVNIHLLSNEKCIETYKDNVTDVMLCAGEMEGGKDTCAGDSGGPLICDGVLQGITSGGATPCAKPKTPAIYAKLIKFTSWIKKVMKENP  246
                                    25        35|       48        58  ||    69     ||79A        89      |||-      | 98       108       118      |130       140       150       160       170       180      |188       198   ||  212       222|      231       241     
                                              35|                    61|          75|  |              95A||     95K                           125|                                                       186A|             202|            222A                        
                                               39                     63           77  |               95B|                                    128                                                        186B              207                                        
                                                                                     79A                95C
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (KLK2_RAT | P00759)
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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  1ton
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  KLK2_RAT | P00759
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