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(-) Description

Title :  CRYSTAL STRUCTURE OF ANIONIC TRYPSIN ISOFORM 2 FROM CHUM SALMON
 
Authors :  D. Iyaguchi, E. Toyota
Date :  28 Jul 08  (Deposition) - 28 Jul 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine Proteinase, Trypsin, Hydrolase, Protease, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Toyota, D. Iyaguchi, H. Sekizaki, M. Tateyama, K. K. Ng
A Structural Comparison Of Three Isoforms Of Anionic Trypsin From Chum Salmon (Oncorhynchus Keta).
Acta Crystallogr. , Sect. D V. 65 717 2009
PubMed-ID: 19564692  |  Reference-DOI: 10.1107/S0907444909012165
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANIONIC TRYPSIN
    ChainsA, B
    Organism CommonCHUM SALMON
    Organism ScientificONCORHYNCHUS KETA
    Organism Taxid8018

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1BEN2Ligand/IonBENZAMIDINE
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:52 , ASN A:54 , GLU A:59 , GLU A:62 , HOH A:2077BINDING SITE FOR RESIDUE CA A 2001
2AC2SOFTWAREGLU B:52 , ASN B:54 , GLU B:59 , GLU B:62 , HOH B:2181BINDING SITE FOR RESIDUE CA B 2002
3AC3SOFTWAREASP A:170 , SER A:171 , GLN A:173 , SER A:176 , TRP A:192 , GLY A:193 , GLY A:195BINDING SITE FOR RESIDUE BEN A 1001
4AC4SOFTWAREASP B:170 , SER B:171 , SER B:176 , SER B:191 , GLY B:195 , GLY B:203BINDING SITE FOR RESIDUE BEN B 1002

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:7 -A:136
2A:25 -A:41
3A:109 -A:209
4A:116 -A:182
5A:147 -A:161
6A:172 -A:196
7B:7 -B:136
8B:25 -B:41
9B:109 -B:209
10B:116 -B:182
11B:147 -B:161
12B:172 -B:196

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZPR)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZPR)

(-) 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:221
 aligned with B3Y8K5_ONCKE | B3Y8K5 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
         B3Y8K5_ONCKE     1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVAVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADGDKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
               SCOP domains d2zpra_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2zprA01     2zprA02 A:13-102,A:210-221 Trypsin-like serine proteases                                  2zprA01 A:1-12,A:103-209 Trypsin-like serine proteases                                                     2zprA02      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeee....eeeehhhhh....eeee............eeeeeeeeee....hhhhh....eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpr A   1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVAVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADGDKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

Chain A from PDB  Type:PROTEIN  Length:221
 aligned with Q8AV11_ONCKE | Q8AV11 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
         Q8AV11_ONCKE     1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
               SCOP domains d2zpra_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2zprA01     2zprA02 A:13-102,A:210-221 Trypsin-like serine proteases                                  2zprA01 A:1-12,A:103-209 Trypsin-like serine proteases                                                     2zprA02      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeee....eeeehhhhh....eeee............eeeeeeeeee....hhhhh....eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpr A   1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVAVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADGDKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with B3Y8K5_ONCKE | B3Y8K5 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
         B3Y8K5_ONCKE     1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVAVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADGDKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
               SCOP domains d2zprb_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2zprB01     2zprB02 B:13-102,B:210-221 Trypsin-like serine proteases                                  2zprB01 B:1-12,B:103-209 Trypsin-like serine proteases                                                     2zprB02      CATH domains
           Pfam domains (1) Trypsin-2zprB01 B:1-215                                                                                                                                                                                                ------ Pfam domains (1)
           Pfam domains (2) Trypsin-2zprB02 B:1-215                                                                                                                                                                                                ------ Pfam domains (2)
         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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpr B   1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVAVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADGDKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q8AV11_ONCKE | Q8AV11 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
         Q8AV11_ONCKE     1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
               SCOP domains d2zprb_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2zprB01     2zprB02 B:13-102,B:210-221 Trypsin-like serine proteases                                  2zprB01 B:1-12,B:103-209 Trypsin-like serine proteases                                                     2zprB02      CATH domains
           Pfam domains (1) Trypsin-2zprB01 B:1-215                                                                                                                                                                                                ------ Pfam domains (1)
           Pfam domains (2) Trypsin-2zprB02 B:1-215                                                                                                                                                                                                ------ Pfam domains (2)
         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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpr B   1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVAVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADGDKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a2zprA01A:1-12,A:103-209
1b2zprB01B:1-12,B:103-209
1c2zprA02A:13-102,A:210-221
1d2zprB02B:13-102,B:210-221

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8AV11_ONCKE | Q8AV11)
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.

Chain A,B   (B3Y8K5_ONCKE | B3Y8K5)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q8AV11_ONCKE | Q8AV112zps
UniProtKB/TrEMBL
        Q8AV11_ONCKE | Q8AV111mbq 2zpq

(-) Related Entries Specified in the PDB File

2zpq ISOFORM 1
2zps ISOFORM 3