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(-) Description

Title :  CRYSTAL STRUCTURE OF A THERMOSTABLE SERINE PROTEASE
 
Authors :  C. A. Smith, H. S. Toogood, H. M. Baker, R. M. Daniel, E. N. Baker
Date :  02 Nov 99  (Deposition) - 18 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Smith, H. S. Toogood, H. M. Baker, R. M. Daniel, E. N. Baker
Calcium-Mediated Thermostability In The Subtilisin Superfamily: The Crystal Structure Of Bacillus Ak. 1 Protease At 1. 8 A Resolution.
J. Mol. Biol. V. 294 1027 1999
PubMed-ID: 10588904  |  Reference-DOI: 10.1006/JMBI.1999.3291
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AK.1 SERINE PROTEASE
    Chains: A
    Organism Scientific: BACILLUS SP. AK1
    Organism Taxid: 268807
    Strain: AK.1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:5 , ASP A:48 , GLU A:83 , ASN A:86 , THR A:88 , ILE A:90BINDING SITE FOR RESIDUE CA A 701
2AC2SOFTWARETYR A:176 , VAL A:179 , ASP A:202 , HOH A:301 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE NA A 702
3AC3SOFTWAREASP A:58 , ASP A:63 , ASP A:65 , HOH A:304 , HOH A:305 , HOH A:306BINDING SITE FOR RESIDUE CA A 703
4AC4SOFTWAREPRO A:47 , ASP A:50 , GLU A:83 , HOH A:307 , HOH A:308 , HOH A:309BINDING SITE FOR RESIDUE CA A 704

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:137 -A:139

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.THES_BACSJ156-167  1A:35-46
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.THES_BACSJ193-203  1A:72-82
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.THES_BACSJ345-355  1A:224-234

(-) Exons   (0, 0)

(no "Exon" information available for 1DBI)

(-) 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:271
 aligned with THES_BACSJ | Q45670 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:280
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401
           THES_BACSJ   122 WTPNDTYYQGYQYGPQNTYTDYAWDVTKGSSGQEIAVIDTGVDYTHPDLDGKVIKGYDFVDNDYDPMDLNNHGTHVAGIAAAETNNATGIAGMAPNTRILAVRALDRNGSGTLSDIADAIIYAADSGAEVINLSLGCDCHTTTLENAVNYAWNKGSVVVAAAGNNGSSTTFEPASYENVIAVGAVDQYDRLASFSNYGTWVDVVAPGVDIVSTITGNRYAYMSGTSMASPHVAGLAALLASQGRNNIEIRQAIEQTADKISGTGTYFKYGRINSYNAVTY 401
               SCOP domains d1dbia_ A: Thermostable serine protease                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dbiA00 A:1-280  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh..hhhhhhhhhh.........eeeeee.............eeeeee............hhhhhhhhhhhh...............eeeeee........hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh..eeeee....---------.....eeeeee.................eeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.............ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SUBTILASE_AS-------------------------SUBTILASE_H---------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dbi A   1 WTPNDTYYQGYQYGPQNTYTDYAWDVTKGSSGQEIAVIDTGVDYTHPDLDGKVIKGYDFVDNDYDPMDLNNHGTHVAGIAAAETNNATGIAGMAPNTRILAVRALDRNGSGTLSDIADAIIYAADSGAEVINLSLGCDCHTTTLENAVNYAWNKGSVVVAAAGNN---------SYENVIAVGAVDQYDRLASFSNYGTWVDVVAPGVDIVSTITGNRYAYMSGTSMASPHVAGLAALLASQGRNNIEIRQAIEQTADKISGTGTYFKYGRINSYNAVTY 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    |    -    |  180       190       200       210       220       230       240       250       260       270       280
                                                                                                                                                                                              165       175
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DBI)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THES_BACSJ | Q45670)
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.
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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