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(-) Description

Title :  TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
 
Authors :  H. -K. S. Leiros, B. O. Brandsdal, O. A. Andersen, V. Os, I. Leiros, R. Helland, J. Otlewski, N. P. Willassen, A. O. Smalas
Date :  09 Dec 03  (Deposition) - 15 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  M
Keywords :  Hydrolase, Trypsin, Inhibitor Specificity, Electrostatic Interactions, Cold-Adaptation, Molecular Dynamics, Binding Free Energy (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -K. S. Leiros, B. O. Brandsdal, O. A. Andersen, V. Os, I. Leiros, R. Helland, J. Otlewski, N. P. Willassen, A. O. Smalas
Trypsin Specificity As Elucidated By Lie Calculations, X-Ray Structures, And Association Constant Measurements
Protein Sci. V. 13 1056 2004
PubMed-ID: 15044735  |  Reference-DOI: 10.1110/PS.03498604

(-) Compounds

Molecule 1 - TRYPSIN I
    Chains: M
    EC Number: 3.4.21.4
    Organ: PYLORIC CAECA
    Organism Common: ATLANTIC SALMON
    Organism Scientific: SALMO SALAR
    Organism Taxid: 8030

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PRA1Ligand/Ion3-PHENYLPROPYLAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU M:70 , ASN M:72 , VAL M:75 , GLU M:77 , GLU M:80 , HOH M:2018BINDING SITE FOR RESIDUE CA M 247
2AC2SOFTWARETYR M:20 , ASP M:189 , SER M:190 , SER M:195 , SER M:214 , TRP M:215 , GLY M:216 , HOH M:2069 , HOH M:2072BINDING SITE FOR RESIDUE PRA M 246
3AC3SOFTWARECYS M:128 , ALA M:129 , PHE M:181 , HOH M:2073BINDING SITE FOR RESIDUE MPD M 248

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1M:22 -M:157
2M:42 -M:58
3M:128 -M:232
4M:136 -M:201
5M:168 -M:182
6M:191 -M:220

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TRY1_SALSA_001 *T33ATRY1_SALSA  ---  ---MP28A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY1_SALSA21-240  1M:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY1_SALSA56-61  1M:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY1_SALSA190-201  1M:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1UTL)

(-) Sequences/Alignments

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 M from PDB  Type:PROTEIN  Length:222
 aligned with TRY1_SALSA | P35031 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:222
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
          TRY1_SALSA     21 IVGGYECKAYSQTHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMASY  242
               SCOP domains d1utlm_ M: Trypsin(ogen)                                                                                                                                                                                                       SCOP domains
               CATH domains 1utlM01     1utlM02 M:28-120,M:233-245 Trypsin-like serine proteases                                  1utlM01 M:16-27,M:121-232 Trypsin-like serine proteases                                                    1utlM02       CATH domains
               Pfam domains Trypsin-1utlM01 M:16-238                                                                                                                                                                                               ------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: M:16-243 UniProt: 21-240                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1utl M   16 IVGGYECKPYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPTSCAPAGTMCTVSGWGNTMSSTADSNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMASY  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150|      161       171       181   |   189       199    || 213   ||  223       233       243  
                                             34|                            67|                                                     125|  ||               150|                             184A 188A             204|     217|  |                        
                                              37                             69                                                      127  ||                152                                                    209      219  |                        
                                                                                                                                        130|                                                                                  221A                        
                                                                                                                                         132
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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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain M   (TRY1_SALSA | P35031)
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.

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  1utl
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  TRY1_SALSA | P35031
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  3.4.21.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRY1_SALSA | P35031: 1bit 1bzx 1hj8 1utj 1utk 1utm 2sta 2stb 2tbs

(-) Related Entries Specified in the PDB File

1bit TRYPSIN (ANIONIC) COMPLEXED WITH THE INHIBITOR BENZAMIDINE
1bzx THE CRYSTAL STRUCTURE OF ANIONIC SALMON TRYPSIN IN COMPLEX WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
1hj8 1.00 AA TRYPSIN FROM ATLANTIC SALMON
1utj TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
1utk TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
1utm TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
1utn TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
1uto TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
1utp TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
1utq TRYPSIN SPECIFICITY AS ELUCIDATED BY LIE CALCULATIONS, X-RAY STRUCTURES AND ASSOCIATION CONSTANT MEASUREMENTS
2sta ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA MAXIMA TRYPSIN INHIBITOR I)
2stb ANIONIC SALMON TRYPSIN IN COMPLEX WITH SQUASH SEED INHIBITOR (CUCURBITA PEPO TRYPSIN INHIBITOR II)
2tbs TRYPSIN COMPLEXED WITH BENZAMIDINE INHIBITOR