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(-) Description

Title :  CRYSTALLOGRAPHIC ANALYSIS OF COUNTER-ION EFFECTS ON SUBTILISIN ENZYMATIC ACTION IN ACETONITRILE (NATIVE DATA)
 
Authors :  M. Cianci, B. Tomaszewki, J. R. Helliwell, P. J. Halling
Date :  09 Oct 09  (Deposition) - 08 Dec 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  E
Keywords :  Serine Protease, Metal-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Cianci, B. Tomaszewski, J. R. Helliwell, P. J. Halling
Crystallographic Analysis Of Counterion Effects On Subtilisin Enzymatic Action In Acetonitrile.
J. Am. Chem. Soc. V. 132 2293 2010
PubMed-ID: 20099851  |  Reference-DOI: 10.1021/JA908703C

(-) Compounds

Molecule 1 - SUBTILISIN CARLSBERG
    Chains: E
    EC Number: 3.4.21.62
    Fragment: RESIDUES 106-379
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CCN5Ligand/IonACETONITRILE
3NA2Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO E:5 , TYR E:6 , ALA E:52 , GLY E:53 , TYR E:256 , SER E:259BINDING SITE FOR RESIDUE SO4 E1276
2AC2SOFTWAREALA E:37 , SER E:38 , HIS E:39 , LEU E:42 , HOH E:2017BINDING SITE FOR RESIDUE NA E1277
3AC3SOFTWAREALA E:169 , TYR E:171 , VAL E:174 , HOH E:2077 , HOH E:2081BINDING SITE FOR RESIDUE NA E1278
4AC4SOFTWAREGLN E:2 , ASP E:41 , LEU E:75 , ASN E:77 , THR E:79 , VAL E:81BINDING SITE FOR RESIDUE CA E1279
5AC5SOFTWARELEU E:126 , GLY E:127 , ALA E:152 , GLY E:154 , HOH E:2121BINDING SITE FOR RESIDUE CCN E1280
6AC6SOFTWAREHIS E:64 , ASN E:218 , HOH E:2071BINDING SITE FOR RESIDUE CCN E1281
7AC7SOFTWAREGLY E:61 , ASN E:62 , ASN E:117 , PRO E:210 , HOH E:2122 , HOH E:2123BINDING SITE FOR RESIDUE CCN E1282
8AC8SOFTWARETYR E:143 , ALA E:243 , SER E:244 , HOH E:2124BINDING SITE FOR RESIDUE CCN E1283
9AC9SOFTWARETHR E:116 , ARG E:145 , HOH E:2125BINDING SITE FOR RESIDUE CCN E1284

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WUW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr E:167 -Pro E:168
2Pro E:210 -Thr E:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.SUBT_BACLI133-144  1E:28-39
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.SUBT_BACLI168-178  1E:64-74
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.SUBT_BACLI323-333  1E:219-229

(-) Exons   (0, 0)

(no "Exon" information available for 2WUW)

(-) 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 E from PDB  Type:PROTEIN  Length:274
 aligned with SUBT_BACLI | P00780 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:274
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    
           SUBT_BACLI   106 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGTYSGIVSGIEWATTNGMDVINMSLGGPSGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTSTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 379
               SCOP domains d2wuwe_ E: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------Peptidase_S8-2wuwE01 E:27-275                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author ...........hhhhhhhh....eeeeeeeee.....................................................eeeeeeee................hhhhhhh...eeee.......hhhhhhhhhhhhhh..eeeee......................eee............................eeee...eeee......hhhhhh.hhhhhhhhh...hhhhhhhhhhhh...............hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS-----------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wuw E   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGNSGSTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "CATH Domain" information available for 2WUW)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (SUBT_BACLI | P00780)
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.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
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
        SUBT_BACLI | P00780: 1af4 1av7 1avt 1be6 1be8 1bfk 1bfu 1c3l 1cse 1oyv 1r0r 1sbc 1sca 1scb 1scd 1scn 1sel 1vsb 1yu6 2sec 2wuv 3unx 3vsb 4c3u 4c3v

(-) Related Entries Specified in the PDB File

1av7 SUBTILISIN CARLSBERG L-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX
1avt SUBTILISIN CARLSBERG D-PARA-CHLOROPHENYL-1- ACETAMIDO BORONIC ACID INHIBITOR COMPLEX
1c3l SUBTILISIN-CARLSBERG COMPLEXED WITH XENON (8 BAR)
1oyv CRYSTAL STRUCTURE OF TOMATO INHIBITOR-II IN A TERNARYCOMPLEX WITH SUBTILISIN CARLSBERG
1r0r 1.1 ANGSTROM RESOLUTION STRUCTURE OF THE COMPLEX BETWEENTHE PROTEIN INHIBITOR, OMTKY3, AND THE SERINE PROTEASE,SUBTILISIN CARLSBERG
1scn SUBTILISIN CARLSBERG COMPLEXED WITH N-(TERT- BUTOXYCARBONYL-ALANYL-PROLYL-PHENYLALANYL)- O- BENZOYL HYDROXYLAMINE
1sel SELENOSUBTILISIN (CHEMICALLY ENGINEERED MUTANT WITH SER 221 REPLACED BY SELENOCYSTEINE)
1vsb SUBTILISIN CARLSBERG L-PARA-CHLOROPHENYL-1- ACETAMIDO BORONIC ACID INHIBITOR COMPLEX
1yu6 CRYSTAL STRUCTURE OF THE SUBTILISIN CARLSBERG :OMTKY3 COMPLEX
2sec SUBTILISIN CARLSBERG COMPLEX WITH GENETICALLY- ENGINEERED N-ACETYL EGLIN-C
2wuv CRYSTALLOGRAPHIC ANALYSIS OF COUNTER-ION EFFECTS ON SUBTILISIN ENZYMATIC ACTION IN ACETONITRILE
3vsb SUBTILISIN CARLSBERG D-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX