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(-) Description

Title :  35/99/170/186/220-LOOPS OF FXA IN SGT
 
Authors :  M. J. Page, E. Di Cera
Date :  08 Jul 09  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Sheets, Serine Protease, Hydrolase, Disulfide Bond, Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Page, E. Di Cera
Combinatorial Enzyme Design Probes Allostery And Cooperativity In The Trypsin Fold.
J. Mol. Biol. V. 399 306 2010
PubMed-ID: 20399789  |  Reference-DOI: 10.1016/J.JMB.2010.04.024

(-) Compounds

Molecule 1 - TRYPSIN
    Chains: A
    EC Number: 3.4.21.4
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PWB980
    Expression System Strain: WB700
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Gene: SPRT
    Mutation: YES
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
    Other Details: 35/99/170/186/220-LOOPS OF FXA IN SGT
    Synonym: SGT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2NA1Ligand/IonSODIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:185 , ASP A:185A , THR A:185B , LYS A:186 , ALA A:221 , ARG A:222 , LYS A:224BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWAREASP A:189 , THR A:190 , GLN A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:219 , GLY A:226 , SO4 A:303BINDING SITE FOR RESIDUE BEN A 302
3AC3SOFTWAREHIS A:57 , GLN A:192 , GLY A:193 , SER A:195 , BEN A:302BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARELYS A:101 , THR A:129BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWAREGLY A:134 , ARG A:169 , ARG A:201BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWARETYR A:185 , ASP A:185A , THR A:185B , LYS A:186BINDING SITE FOR RESIDUE SO4 A 306

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:168 -A:182
3A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I78)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I78)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYP_STRGR37-257  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYP_STRGR69-74  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYP_STRGR202-213  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 3I78)

(-) 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:229
 aligned with TRYP_STRGR | P00775 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:230
                                                                                                                116                                                                                                                                               
                                               57    58                                                      115  |                                                                                                                                               
                                    46        56|     | 61        71        81        91       101       111   |  |119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
          TRYP_STRGR     37 VVGGTRAAQGEFPFMVRLSMG-----CGGALYAQDIVLTAAHCVSGSGNNTSITATGGVVDLQSSSAVKVRSTKVLQAPGYNGT--GKDWALIKLAQPINQPTLKIATTTAYNQGTFTVAGWGANREGGSQQRYLLKANVPFVSDAACRSAYGNELVANEEICAGYPDTGGVDTCQGDSGGPMFRKDNADEWIQVGIVSWGYGCARPGYPGVYTEVSTFASAIASAARTL  259
               SCOP domains d3i78a_ A: Trypsin                                                                                                                                                                                                                     SCOP domains
               CATH domains 3i78A01     3i78A02 A:28-120,A:233-245 Trypsin-like serine proteases                                   3i78A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                           3i78A02       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeeee..eeeehhhhh...ee...eeeee..........eeeeeeeeee.............eeeee.........ee.........eeeeee..............eeeeeeeehhhhhhhhh........eeee..-..............eeeee.....eeeeeeeeee.........eeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 37-257                                                                                                                                                                                          -- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3i78 A   16 VVGGTRAAQGEFPFMVRLINEENEGFCGGALYAQDIVLTAAHCVSGSGNNTSITATGGVVDLQSSSAVKVRSTKVLQAPGFTKETYGKDWALIKLAQPINQPTLKIATTTAYNQGTFTVAGWGANREGGSQQRYLLKANVPFVSDAACRSSSSFILVANEMICAGY-DTKQEDTCQGDSGGPMFRKDNADEWVQVGIVSWGEGCARKGKYGVYTEVSTFASAIASAARTL  245
                                    25        35        45        55     |||61        71 || ||  83        93       103       113|      129       139      |150       160       170       179     | 186       196       205       215 ||    225       235       245
                                                                       60A|||           73| ||                               113|    125|               146|                          177A     185 ||                204A          217| 223A                      
                                                                        60B||            75 ||                                118     128                148                                    185A|                               219                           
                                                                         60C|              77|                                                                                                   185B                                                             
                                                                          60D               79
   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 3I78)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRYP_STRGR | P00775)
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: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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  3i78
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  TRYP_STRGR | P00775
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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
        TRYP_STRGR | P00775: 1os8 1oss 1sgt 2fmj 3beu 3i77

(-) Related Entries Specified in the PDB File

1os8 WILD-TYPE SGT
2fmj 220-LOOP OF FXA IN SGT
3beu 99/170/186/220-LOOPS OF FXA IN SGT
3i77 35/99/170-LOOPS OF FXA IN SGT