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(-) Description

Title :  ANIONIC TRYPSIN VARIANT S195A IN COMPLEX WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) CLEAVED AT THE SCISSILE BOND (LYS15-ALA16) DETERMINED TO THE 1.46 A RESOLUTION LIMIT
 
Authors :  E. Zakharova, M. P. Horvath, D. P. Goldenberg
Date :  04 Jan 09  (Deposition) - 17 Feb 09  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  E,I,J
Keywords :  Enzyme-Inhibitor Complex, Peptide Bond Hydrolysis, Calcium, Digestion, Hydrolase, Metal-Binding, Protease, Secreted, Serine Protease, Zymogen, Pharmaceutical, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Zakharova, M. P. Horvath, D. P. Goldenberg
Structure Of A Serine Protease Poised To Resynthesize A Peptide Bond.
Proc. Natl. Acad. Sci. Usa V. 106 11034 2009
PubMed-ID: 19549826  |  Reference-DOI: 10.1073/PNAS.0902463106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANIONIC TRYPSIN-2
    Chains: E
    EC Number: 3.4.21.4
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Plasmid: PYT
    Expression System Strain: DLM101
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: PRSS2, TRY2
    Mutation: YES
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: ANIONIC TRYPSIN II, PRETRYPSINOGEN II, SERINE PROTEASE 2
 
Molecule 2 - PANCREATIC TRYPSIN INHIBITOR
    Chains: I
    Engineered: YES
    Other Details: BOVINE PANCREATIC TRYPSIN INHIBITOR WAS OBTAINED IN ITS HYDROLYZED FORM BY PARTIAL REDUCTION AT THE CYS14-CYS38 DISULFIDE, TREATMENT WITH TRYPSIN, PURIFICATION BY HPLC AND RE-OXIDATION OF THE CYS14-CYS38 DISULFIDE
    Synonym: BASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ
    Synthetic: YES
 
Molecule 3 - PANCREATIC TRYPSIN INHIBITOR
    Chains: J
    Engineered: YES
    Synonym: BASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : EIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN E:34 , GLY E:38 , TYR E:39 , HIS E:40 , ARG E:67 , ILE E:73 , ASN E:74 , HOH E:794 , HOH E:843BINDING SITE FOR RESIDUE EDO E 501
02AC2SOFTWAREILE E:47 , ASN E:48 , LEU E:123 , GLN E:239 , ILE E:242 , HOH E:793 , HOH E:830BINDING SITE FOR RESIDUE EDO E 502
03AC3SOFTWARELYS E:97 , THR E:98 , LYS E:175 , TYR E:217 , HOH E:799 , HOH E:818 , HOH E:927 , HOH E:961 , PRO I:13 , ARG J:39BINDING SITE FOR RESIDUE EDO E 503
04AC4SOFTWAREGLY E:216 , TYR E:217 , GLY E:219 , ASP I:3 , TYR I:10 , GLY I:12 , EDO I:505 , HOH I:707 , HOH I:709 , HOH I:723BINDING SITE FOR RESIDUE EDO E 504
05AC5SOFTWAREGLY E:18 , PHE E:184A , GLU E:186 , GLY E:187 , GLY E:188 , LYS E:188A , HOH E:739BINDING SITE FOR RESIDUE PG4 E 506
06AC6SOFTWAREGLU E:70 , ASN E:72 , VAL E:75 , GLU E:77 , GLU E:80 , HOH E:708 , HOH E:907BINDING SITE FOR RESIDUE CA E 601
07AC7SOFTWAREEDO E:504 , ASP I:3 , PHE I:4 , TYR I:10 , LYS J:41 , SO4 J:603BINDING SITE FOR RESIDUE EDO I 505
08AC8SOFTWAREHOH E:808 , ARG J:20 , TYR J:35 , GLY J:37 , ALA J:40 , HOH J:711 , HOH J:717 , HOH J:719 , HOH J:735BINDING SITE FOR RESIDUE SO4 J 602
09AC9SOFTWAREEDO I:505 , LYS J:41 , ARG J:42 , HOH J:703 , HOH J:708 , HOH J:731 , HOH J:746BINDING SITE FOR RESIDUE SO4 J 603
10BC1SOFTWARELYS E:175 , HOH I:711 , ARG J:39 , ARG J:42BINDING SITE FOR RESIDUE SO4 J 604
11BC2SOFTWAREILE J:18 , ILE J:19 , ARG J:20 , HOH J:745 , HOH J:748 , HOH J:749BINDING SITE FOR RESIDUE SO4 J 605

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1E:22 -E:157
2E:42 -E:58
3E:128 -E:232
4E:136 -E:201
5E:168 -E:182
6E:191 -E:220
7I:5 -J:55
8I:14 -J:38
9J:30 -J:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FP7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FP7)

(-) PROSITE Motifs  (5, 5)

Asymmetric/Biological Unit (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY2_RAT24-244  1E:16-243
2BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90  1I:5-15
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY2_RAT59-64  1E:53-58
4BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86  1J:33-51
5TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY2_RAT194-205  1E:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000188521ENSRNOE00000331572chr4:69088288-6908832740TRY2_RAT1-14140--
1.2bENSRNOT000000188522bENSRNOE00000277233chr4:69090744-69090903160TRY2_RAT14-67541E:16-61 (gaps)46
1.3ENSRNOT000000188523ENSRNOE00000105498chr4:69092114-69092367254TRY2_RAT67-152861E:61-149 (gaps)89
1.4ENSRNOT000000188524ENSRNOE00000338303chr4:69092772-69092908137TRY2_RAT152-197461E:149-19246
1.5ENSRNOT000000188525ENSRNOE00000134316chr4:69093163-69093367205TRY2_RAT198-246491E:193-245 (gaps)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 E 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 d3fp7e_ E: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 3fp7E01     3fp7E02 E:28-120,E:233-245 Trypsin-like serine proteases                                  3fp7E01 E:16-27,E:121-232 Trypsin-like serine proteases                                                     3fp7E02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: E:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.2b  PDB: E:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: E:149-192 UniProt: 152-197     Exon 1.5  PDB: E:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: E:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                3fp7 E   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDAGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57      ||68        78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                         64|                                                        125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                          66                                                         127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221A                        
                                                                                                                                         132                                                                                                               


Chain I from PDB  Type:PROTEIN  Length:15
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:15
                                    45     
          BPT1_BOVIN     36 RPDFCLEPPYTGPCK   50
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                PROSITE (2) ----BPTI_KUNITZ PROSITE (2)
                PROSITE (3) --------------- PROSITE (3)
                 Transcript --------------- Transcript
                3fp7 I    1 RPDFCLEPPYTGPCK   15
                                    10     


Chain J from PDB  Type:PROTEIN  Length:43
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:43
                                    60        70        80        90   
          BPT1_BOVIN     51 ARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA   93
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee...........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                PROSITE (2) BPTI_KUNITZ_2  PDB: - UniProt: 40-90    --- PROSITE (2)
                PROSITE (3) -----------------BPTI_KUNITZ_1      ------- PROSITE (3)
                 Transcript ------------------------------------------- Transcript
                3fp7 J   16 ARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA   58
                                    25        35        45        55
   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, 1)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FP7)

(-) Gene Ontology  (21, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (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.

Chain I,J   (BPT1_BOVIN | P00974)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0019870    potassium channel inhibitor activity    Stops, prevents, or reduces the activity of a potassium channel.
    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:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0090331    negative regulation of platelet aggregation    Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0070495    negative regulation of thrombin-activated receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of thrombin-activated receptor protein signaling pathway activity. A thrombin receptor signaling pathway is the series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
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.

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  3fp7
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  BPT1_BOVIN | P00974
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  TRY2_RAT | P00763
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 Related Entries

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

UniProtKB/Swiss-Prot
        BPT1_BOVIN | P00974: 1aal 1b0c 1bhc 1bpi 1bpt 1brb 1bth 1bti 1bz5 1bzx 1cbw 1co7 1d0d 1eaw 1ejm 1f5r 1f7z 1fak 1fan 1fy8 1g6x 1jv8 1jv9 1k09 1k6u 1ld5 1ld6 1mtn 1nag 1oa5 1oa6 1p2i 1p2j 1p2k 1p2m 1p2n 1p2o 1p2q 1pit 1qlq 1t7c 1t8l 1t8m 1t8n 1t8o 1tpa 1uua 1uub 1ykt 1ylc 1yld 2fi3 2fi4 2fi5 2ftl 2ftm 2hex 2ijo 2kai 2ptc 2r9p 2ra3 2tgp 2tpi 2zjx 2zvx 3btd 3bte 3btf 3btg 3bth 3btk 3btm 3btq 3btt 3btw 3fp6 3fp8 3gym 3ldi 3ldj 3ldm 3otj 3p92 3p95 3tgi 3tgj 3tgk 3tpi 3u1j 3wny 4bnr 4dg4 4pti 4tpi 4wwy 4wxv 4y0y 4y0z 4y10 4y11 5jb4 5jb5 5jb6 5jb7 5pti 6pti 7pti 8pti 9pti
        TRY2_RAT | P00763: 1amh 1anb 1anc 1and 1ane 1bra 1brb 1brc 1co7 1dpo 1ezs 1ezu 1f5r 1f7z 1fy8 1j14 1j15 1j16 1j17 1k9o 1ql9 1slu 1slv 1slw 1slx 1trm 1ykt 1ylc 1yld 2trm 3fp6 3fp8 3tgi 3tgj 3tgk

(-) Related Entries Specified in the PDB File

3fp6 ANIONIC TRYPSIN IN COMPLEX WITH BPTI DETERMINED TO THE 1.49 A RESOLUTION LIMIT
3fp8 ANIONIC TRYPSIN VARIANT S195A IN COMPLEX WITH BPTI DETERMINED TO THE 1.46 A RESOLUTION LIMIT
3tgi ANIONIC TRYPSIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) DETERMINED TO THE 1.8 A RESOLUTION LIMIT