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(-) Description

Title :  THE 1.8 A CRYSTAL STRUCTURE OF A PROTEINASE K LIKE ENZYME FROM A PSYCHROTROPH SERRATIA SPECIES
 
Authors :  R. Helland, A. N. Larsen, A. O. Smalas, N. P. Willassen
Date :  03 Oct 05  (Deposition) - 07 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  S Binding, Substrate Specificity, Proteinase K, Subtilase, Psychrotrophic, Psychrophilic, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Helland, A. N. Larsen, A. O. Smalas, N. P. Willassen
The 1. 8 A Crystal Structure Of A Proteinase K-Like Enzyme From A Psychrotroph Serratia Species
Febs J. V. 273 61 2006
PubMed-ID: 16367748  |  Reference-DOI: 10.1111/J.1742-4658.2005.05040.X

(-) Compounds

Molecule 1 - PROTEINASE K
    Chains: A
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD-GIII
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-277
    Organism Scientific: SERRATIA SP.
    Organism Taxid: 348903
    Strain: GF96
 
Molecule 2 - TRIPEPTIDE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SERRATIA SP.
    Organism Taxid: 348903
    Other Details: THE PEPTIDE IS ASSUMED TO BE A PROTEOLYSIS PRODUCT EITHER FROM THE EXPRESSION OR PURIFICATION PROCESS.
    Strain: GF96

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:11 , ASP A:14 , GLN A:15 , ASP A:21 , ASN A:23 , HOH A:432BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWARETHR A:184 , SER A:190 , SER A:191 , SER A:206 , HOH A:548BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREASN A:60C , LYS A:265 , THR A:266 , HOH A:423BINDING SITE FOR RESIDUE SO4 A 302

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:98
2A:167 -A:198

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:18 -Pro A:19
2Ser A:170 -Pro A:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B6N)

(-) Exons   (0, 0)

(no "Exon" information available for 2B6N)

(-) 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:278
 aligned with Q3HUQ2_9GAMM | Q3HUQ2 from UniProtKB/TrEMBL  Length:629

    Alignment length:278
                                   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396        
        Q3HUQ2_9GAMM    127 ADQPSPTWGIDRIDQRNLPLDNNYHTDYDGSGVTAFVIDTGVLNTHNEFGGRASSGYDFIDNDYDATDCNGHGTHVAGTIGGSTYGVAKNVNVVGVRVLNCSGSGSNSGVIAGINWVKNNASGPAVANMSLGGGASQATDDAVNAAVAAGITFVVAAGNDNSNACNYSPARAADAITVGSTTSNDSRSSFSNYGTCLDIYAPGSSITSSWYTSNSATNTISGTSMASPHVAGVAALYLDENPNLSPAQVTNLLKTRATADKVTDAKTGSPNKLLFSLA  404
               SCOP domains d2b6na_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2b6nA00 A:1-277  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhh........eee........eeeeee......hhhhh..eeeeee............hhhhhhhhhhhh.........eeeeee........hhhhhhhhhhhhhhhh...eeeee...ee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.................eeee...eeee.......eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhee............ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b6n A    1 ADQPSPTWGIDRIDQRNLPLDNNYHTDYDGSGVTAFVIDTGVLNTHNEFGGRASSGYDFIDNDYDATDCNGHGTHVAGTIGGSTYGVAKNVNVVGVRVLNCSGSGSNSGVIAGINWVKNNASGPAVANMSLGGGASQATDDAVNAAVAAGITFVVAAGNDNSNACNYSPARAADAITVGSTTSNDSRSSFSNYGTCLDIYAPGSSITSSWYTSNSATNTISGTSMASPHVAGVAALYLDENPNLSPAQVTNLLKTRATADKVTDAKTGSPNKLLFSLA  277
                                    10        20        30        40        50        60|||     67        77        87        97       107       117 ||    132       142       152       162       172       182       192       202       212 ||    220       230       240 |     249       259       269        
                                                                                      60B||                                                        119|                                                                                     213B|                         241B                                    
                                                                                       60C|                                                         125                                                                                      213C                                                                 
                                                                                        60D                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:3
                                    
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                2b6n B    1 APT    3
   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: 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 2B6N)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q3HUQ2_9GAMM | Q3HUQ2)
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.

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