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(-) Description

Title :  CRYSTAL STRUCTURE OF A COLD ADAPTED SUBTILISIN-LIKE SERINE PROTEINASE
 
Authors :  J. Arnorsdottir, M. M. Kristjansson, R. Ficner
Date :  09 Jan 04  (Deposition) - 22 Feb 05  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Arnorsdottir, M. M. Kristjansson, R. Ficner
Crystal Structure Of A Subtilisin-Like Serine Proteinase From A Psychrotrophic Vibrio Species Reveals Structural Aspects Of Cold Adaptation.
Febs J. V. 272 832 2005
PubMed-ID: 15670163  |  Reference-DOI: 10.1111/J.1742-4658.2005.04523.X

(-) Compounds

Molecule 1 - EXTRACELLULAR SUBTILISIN-LIKE SERINE PROTEINASE
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD TOPO
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: VIBRIO SP. PA-44
    Organism Taxid: 210249

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2PMS2Ligand/IonPHENYLMETHANESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PMS1Ligand/IonPHENYLMETHANESULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PMS1Ligand/IonPHENYLMETHANESULFONIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:171 , GLY A:173 , ASP A:196 , HOH A:1369 , HOH A:1412 , HOH A:1416BINDING SITE FOR RESIDUE CA A 1290
2AC2SOFTWAREASP A:56 , ASP A:61 , ASP A:63 , HOH A:1422 , HOH A:1449BINDING SITE FOR RESIDUE CA A 1291
3AC3SOFTWAREASP A:9 , ASP A:12 , GLN A:13 , ASP A:19 , ASN A:21 , HOH A:1437BINDING SITE FOR RESIDUE CA A 1292
4AC4SOFTWAREPRO B:171 , GLY B:173 , ASP B:196 , HOH B:2383 , HOH B:2389 , HOH B:2445 , HOH B:2450BINDING SITE FOR RESIDUE CA B 2290
5AC5SOFTWAREASP B:56 , ASP B:61 , ASP B:63 , HOH B:2390 , HOH B:2423BINDING SITE FOR RESIDUE CA B 2291
6AC6SOFTWAREASP B:9 , ASP B:12 , GLN B:13 , ASP B:19 , ASN B:21 , HOH B:2329BINDING SITE FOR RESIDUE CA B 2292
7AC7SOFTWAREHIS A:70 , LEU A:129 , GLY A:130 , GLY A:156 , ASN A:157 , THR A:219 , SER A:220BINDING SITE FOR RESIDUE PMS A 1284
8AC8SOFTWARESER B:128 , ASN B:157 , SER B:220 , HOH B:2376BINDING SITE FOR RESIDUE PMS B 2284

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:67 -A:99
2A:163 -A:194
3A:277 -A:281
4B:67 -B:99
5B:163 -B:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:16 -Pro A:17
2Ser A:166 -Pro A:167
3Leu B:16 -Pro B:17
4Ser B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S2N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S2N)

(-) Exons   (0, 0)

(no "Exon" information available for 1S2N)

(-) Sequences/Alignments

Asymmetric 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:281
 aligned with Q8GB52_9VIBR | Q8GB52 from UniProtKB/TrEMBL  Length:530

    Alignment length:281
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419 
         Q8GB52_9VIBR   140 QSNAIWGLDRIDQRNLPLDRNYNANFDGFGVTAYVIDTGVNNNHEEFGGRSVSGYDFVDNDADSSDCNGHGTHVAGTIGGSQYGVAKNVNIVGVRVLSCSGSGTTSGVISGVDWVAQNASGPSVANMSLGGGQSTALDSAVQGAIQSGVSFMLAAGNSNADACNTSPARVPSGVTVGSTTSSDSRSSFSNWGSCVDLFAPGSQIKSAWYDGGYKTISGTSMATPHVAGVAALYLQENNGLTPLQLTGLLNSRASENKVSDTRGTTNKLLYSLADSGCEPDC 420
               SCOP domains d1s2na_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1s2nA00 A:1-281  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh...................eeeeee.............eeeeee............hhhhhhhhhhhh.........eeeeee........hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh..eeeee......hhhhh........eeeeee.................eeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhee...........ee........hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2n A   1 QSNAIWGLDRIDQRNLPLDRNYNANFDGFGVTAYVIDTGVNNNHEEFGGRSVSGYDFVDNDADSSDCNGHGTHVAGTIGGSQYGVAKNVNIVGVRVLSCSGSGTTSGVISGVDWVAQNASGPSVANMSLGGGQSTALDSAVQGAIQSGVSFMLAAGNSNADACNTSPARVPSGVTVGSTTSSDSRSSFSNWGSCVDLFAPGSQIKSAWYDGGYKTISGTSMATPHVAGVAALYLQENNGLTPLQLTGLLNSRASENKVSDTRGTTNKLLYSLADSGCEPDC 281
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280 


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with Q8GB52_9VIBR | Q8GB52 from UniProtKB/TrEMBL  Length:530

    Alignment length:273
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410   
         Q8GB52_9VIBR   141 SNAIWGLDRIDQRNLPLDRNYNANFDGFGVTAYVIDTGVNNNHEEFGGRSVSGYDFVDNDADSSDCNGHGTHVAGTIGGSQYGVAKNVNIVGVRVLSCSGSGTTSGVISGVDWVAQNASGPSVANMSLGGGQSTALDSAVQGAIQSGVSFMLAAGNSNADACNTSPARVPSGVTVGSTTSSDSRSSFSNWGSCVDLFAPGSQIKSAWYDGGYKTISGTSMATPHVAGVAALYLQENNGLTPLQLTGLLNSRASENKVSDTRGTTNKLLYSLAD 413
               SCOP domains d1s2nb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1s2nB00 B:2-274  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) ------------------------------Peptidase_S8-1s2nB01 B:32-274                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) ------------------------------Peptidase_S8-1s2nB02 B:32-274                                                                                                                                                                                                                       Pfam domains (2)
         Sec.struct. author ...hhhhhhhh...................eeeeee.............eeeeee............hhhhhhhhhhhh.........eeeeee........hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh..eeeee......hhhhh........eeeeee.................eeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhee...........ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2n B   2 SNAIWGLDRIDQRNLPLDRNYNANFDGFGVTAYVIDTGVNNNHEEFGGRSVSGYDFVDNDADSSDCNGHGTHVAGTIGGSQYGVAKNVNIVGVRVLSCSGSGTTSGVISGVDWVAQNASGPSVANMSLGGGQSTALDSAVQGAIQSGVSFMLAAGNSNADACNTSPARVPSGVTVGSTTSSDSRSSFSNWGSCVDLFAPGSQIKSAWYDGGYKTISGTSMATPHVAGVAALYLQENNGLTPLQLTGLLNSRASENKVSDTRGTTNKLLYSLAD 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8GB52_9VIBR | Q8GB52)
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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 Related Entries

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        Q8GB52_9VIBR | Q8GB52: 1sh7

(-) Related Entries Specified in the PDB File

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