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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CA6 SITE MUTANT OF PRO-SA-SUBTILISIN
 
Authors :  R. Uehara, Y. Takeuchi, S. Tanaka, H. Matsumura, Y. Koga, K. Takano, S. K
Date :  01 Sep 11  (Deposition) - 11 Jul 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Proteolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Uehara, Y. Takeuchi, S. I. Tanaka, K. Takano, Y. Koga, S. Kanaya
Requirement Of Ca(2+) Ions For The Hyperthermostability Of Tk-Subtilisin From Thermococcus Kodakarensis
Biochemistry V. 51 5369 2012
PubMed-ID: 22686281  |  Reference-DOI: 10.1021/BI300427U

(-) Compounds

Molecule 1 - TK-SUBTILISIN
    Chains: A
    EC Number: 3.4.21.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: TK1675
    Mutation: YES
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:108 , GLN A:110 , ALA A:227 , GLU A:229 , HOH A:413 , HOH A:420BINDING SITE FOR RESIDUE CA A 399
2AC2SOFTWARELEU A:205 , ASP A:208 , VAL A:210 , ASP A:226 , HOH A:406 , HOH A:578BINDING SITE FOR RESIDUE CA A 400
3AC3SOFTWAREASP A:212 , ASP A:214 , ASP A:216 , ILE A:218 , ASP A:222 , ASP A:225BINDING SITE FOR RESIDUE CA A 401
4AC4SOFTWAREGLN A:84 , ASP A:124 , LEU A:164 , ASN A:166 , ILE A:168 , VAL A:170BINDING SITE FOR RESIDUE CA A 402
5AC5SOFTWAREASP A:214 , ASP A:216 , ASP A:222 , ASP A:224BINDING SITE FOR RESIDUE CA A 403

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:132 -A:147

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:272 -Pro A:273
2Pro A:313 -Asp A:314

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.TKSU_THEKO135-146  1A:111-122
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TKSU_THEKO346-356  1A:322-332

(-) Exons   (0, 0)

(no "Exon" information available for 3VHQ)

(-) 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:385
 aligned with TKSU_THEKO | P58502 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:395
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417     
           TKSU_THEKO    28 NTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSWLGGGSTQPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDDAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTSMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 422
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhh..eeeee.....eeeeeee..hhhhhhh...eeeeee..eeee..ee..-------.....hhhhhhh.hhhhh..........eeeeee.........hhh.eeeeee.hhhh...hhhhhh...hhhhhhhhhhhh..............eeeeee......eeehhhhhhhhhhhhhh.......................eeee.ee....hhhhhhhhhhhhhh..eeeee.................eeeeeee...............eeee...eeeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhh...---...........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------SUBTILASE_AS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vhq A   4 NTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSW-------PAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDDAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTAMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADAL---GWDADYGYGVVRAALAVQAALG 398
                                    13        23        33        43        53        63        73|       83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   |   383       393     
                                                                                                 74      82                                                                                                                                                                                                                                                                                                373 377
   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  (0, 0)

(no "SCOP Domain" information available for 3VHQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VHQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TKSU_THEKO | P58502)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TKSU_THEKO | P58502: 2e1p 2z2x 2z2y 2z2z 2z30 2z56 2z57 2z58 2zrq 2zwo 2zwp 3a3n 3a3o 3a3p 3vv2 3wiu 3wiv 4jp8

(-) Related Entries Specified in the PDB File

2e1p CRYSTAL STRUCTURE OF UNAUTOPROCESSED FORM2 OF TK-SUBTILISIN
2zwo CRYSTAL STRUCTURE OF THE CA2 SITE MUTANT OF PRO-SA- SUBTILISIN
2zwp CRYSTAL STRUCTURE OF THE CA3 SITE MUTANT OF PRO-SA- SUBTILISIN