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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE OF ASP102 IN SERINE PROTEASE CATALYSIS
 
Authors :  S. Sprang, T. Standing, R. J. Fletterick
Date :  21 Oct 87  (Deposition) - 16 Jul 88  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Serine Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sprang, T. Standing, R. J. Fletterick, R. M. Stroud, J. Finer-Moore, N. H. Xuong, R. Hamlin, W. J. Rutter, C. S. Craik
The Three-Dimensional Structure Of Asn102 Mutant Of Trypsin: Role Of Asp102 In Serine Protease Catalysis.
Science V. 237 905 1987
PubMed-ID: 3112942
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN
    ChainsA, B
    EC Number3.4.21.4
    EngineeredYES
    Organism CommonBLACK RAT
    Organism ScientificRATTUS RATTUS
    Organism Taxid10117

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:271BINDING SITE FOR RESIDUE CA A 247
2AC2SOFTWAREGLU B:70 , ASN B:72 , VAL B:75 , GLU B:77 , GLU B:80 , HOH B:272BINDING SITE FOR RESIDUE CA B 247
3AC3SOFTWAREASP A:189 , SER A:190 , GLN A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:219 , GLY A:226BINDING SITE FOR RESIDUE BEN A 246
4AC4SOFTWAREASP B:189 , SER B:190 , GLN B:192 , SER B:195 , VAL B:213 , GLY B:216 , GLY B:219 , CYS B:220 , GLY B:226BINDING SITE FOR RESIDUE BEN B 246
5CTAAUTHORHIS A:57 , ASN A:102 , SER A:195CATALYTIC SITE IN CHAIN A
6CTBAUTHORHIS B:57 , ASN B:102 , SER B:195CATALYTIC SITE IN CHAIN B

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:128 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220
7B:22 -B:157
8B:42 -B:58
9B:128 -B:232
10B:136 -B:201
11B:168 -B:182
12B:191 -B:220

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY2_RAT24-244
 
  2A:16-243
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY2_RAT59-64
 
  2A:53-58
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY2_RAT194-205
 
  2A:189-200
B:189-200

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000188521ENSRNOE00000331572chr4:69088288-6908832740TRY2_RAT1-14140--
1.2bENSRNOT000000188522bENSRNOE00000277233chr4:69090744-69090903160TRY2_RAT14-67542A:16-61 (gaps)
B:16-61 (gaps)
46
46
1.3ENSRNOT000000188523ENSRNOE00000105498chr4:69092114-69092367254TRY2_RAT67-152862A:61-149 (gaps)
B:61-149 (gaps)
90
90
1.4ENSRNOT000000188524ENSRNOE00000338303chr4:69092772-69092908137TRY2_RAT152-197462A:149-192
B:149-192
46
46
1.5ENSRNOT000000188525ENSRNOE00000134316chr4:69093163-69093367205TRY2_RAT198-246492A:193-245 (gaps)
B:193-245 (gaps)
54
54

(-) 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 A from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1trma_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1trmA01     1trmA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1trmA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1trmA02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ....e....................eee......eeee.......eeeee............eeeee.eeeee...........eeeee..........................eeeee...............eeeeee..hhhhhhhhh......eeeee...............eeeee..eeeeeeee..........----hhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee-------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: A:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: A:149-192 UniProt: 152-197     Exon 1.5  PDB: A:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1trm A   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNNIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57        66|       78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                          65A||                                                     125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                            66|                                                      127  ||                                                                        209      219  |                        
                                                                             69                                                         130|                                                                                   221A                        
                                                                                                                                         132                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1trmb_ B: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1trmB01     1trmB02 B:28-120,B:233-245 Trypsin-like serine proteases                                  1trmB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                     1trmB02       CATH domains
           Pfam domains (1) Trypsin-1trmB01 B:16-238                                                                                                                                                                                                ------- Pfam domains (1)
           Pfam domains (2) Trypsin-1trmB02 B:16-238                                                                                                                                                                                                ------- Pfam domains (2)
     Sec.struct. author (1) ....e....................eee......eeee.......eeeee............eeeee.eeeee...........eeeee..........................eeeee...............eeeeee..hhhhhhhhh......eeeee...............eeeee..eeeeeeee..........----hhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee-------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: B:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: B:149-192 UniProt: 152-197     Exon 1.5  PDB: B:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: B:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1trm B   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNNIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57        66|       78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
1a1trmA01A:16-27,A:121-232
1b1trmA02A:28-120,A:233-245
1c1trmB02B:28-120,B:233-245
1d1trmB01B:16-27,B:121-232

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRY2_RAT | P00763)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    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.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TRY2_RAT | P007631amh 1anb 1anc 1and 1ane 1bra 1brb 1brc 1co7 1dpo 1ezs 1ezu 1f5r 1f7z 1fy8 1j14 1j15 1j16 1j17 1k9o 1ql9 1slu 1slv 1slw 1slx 1ykt 1ylc 1yld 2trm 3fp6 3fp7 3fp8 3tgi 3tgj 3tgk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TRM)