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(-) Description

Title :  EXTRACELLULAR NUCLEASE
 
Authors :  J. E. Korczynska, J. P. Turkenburg, E. J. Taylor
Date :  08 Jun 10  (Deposition) - 20 Jul 11  (Release) - 25 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Korczynska, J. P. Turkenburg, E. J. Taylor
The Structural Characterization Of A Prophage- Encoded Extracellular Dnase From Streptococcus Pyogenes.
Nucleic Acids Res. V. 40 928 2012
PubMed-ID: 21948797  |  Reference-DOI: 10.1093/NAR/GKR789

(-) Compounds

Molecule 1 - SPD1 NUCLEASE
    Atcc: 700294
    Chains: A, B
    EC Number: 3.1.21.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIPL
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Strain: GAS-SF370
    Synonym: PUTATIVE DNASE

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP B:115 , MET B:117 , ASN B:118 , MET B:140 , THR B:141 , ALA B:142 , TRP B:143 , ALA B:236BINDING SITE FOR RESIDUE PEG B1252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XH3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XH3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XH3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XH3)

(-) Exons   (0, 0)

(no "Exon" information available for 2XH3)

(-) 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:179
 aligned with Q9A0M1_STRP1 | Q9A0M1 from UniProtKB/TrEMBL  Length:252

    Alignment length:205
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247     
         Q9A0M1_STRP1    48 TVSSKLLPFTANYQLQLGELDNLNRATFSHIQLQDRHETKDVRTKINYDPVGWHNYQFPYGDGSKSSWVMNRGHLVGYQFCGLNDEPRNLVAMTAWLNTGAYSGANDSNPEGMLYYENRLDSWLALHPDFWLDYKVTPIYSGNEVVPRQIELQYVGIDSSGELLTIRLNSNKESIDENGVTTVILENSAPNINLDYLNGTATPKN 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee...........eeeeehhhhh.--------------------------..ee..eee..hhhhhh...hhh.eee.hhhhhhh............hhhhhhhhhhhhhhh...eeeeeeeee.........eeeeeeeee.....ee.........ee.....eeeeee.....eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xh3 A  48 TVSSKLLPFTANYQLQLGELDNLNRATFSHIQLQDRHET--------------------------SSWVMNRGHLVGYQFCGLNDEPRNLVAMTAWLATGAYSGANDSNPEGMLYYENRLDSWLALHPDFWLDYKVTPIYSGNEVVPRQIELQYVGIDSSGELLTIRLNSNKESIDENGVTTVILENSAPNINLDYLNGTATPKN 252
                                    57        67        77        |-         -         -     | 117       127       137       147       157       167       177       187       197       207       217       227       237       247     
                                                                 86                        113                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with Q9A0M1_STRP1 | Q9A0M1 from UniProtKB/TrEMBL  Length:252

    Alignment length:203
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248   
         Q9A0M1_STRP1    49 VSSKLLPFTANYQLQLGELDNLNRATFSHIQLQDRHETKDVRTKINYDPVGWHNYQFPYGDGSKSSWVMNRGHLVGYQFCGLNDEPRNLVAMTAWLNTGAYSGANDSNPEGMLYYENRLDSWLALHPDFWLDYKVTPIYSGNEVVPRQIELQYVGIDSSGELLTIRLNSNKESIDENGVTTVILENSAPNINLDYLNGTATPK 251
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee...........eeeee......--------------------------..ee..eee..hhhhhh...hhh.eee.hhhhhhh............hhhhhhhhhhhhhhh...eeeeeeeee.........eeeeeeeee.....ee........eee.....eeeeee......eee....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xh3 B  49 VSSKLLPFTANYQLQLGELDNLNRATFSHIQLQDRHET--------------------------SSWVMNRGHLVGYQFCGLNDEPRNLVAMTAWLATGAYSGANDSNPEGMLYYENRLDSWLALHPDFWLDYKVTPIYSGNEVVPRQIELQYVGIDSSGELLTIRLNSNKESIDENGVTTVILENSAPNINLDYLNGTATPK 251
                                    58        68        78       | -         -         -    |  118       128       138       148       158       168       178       188       198       208       218       228       238       248   
                                                                86                        113
   Legend:   → Mismatch (orange background)
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  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 2XH3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XH3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XH3)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9A0M1_STRP1 | Q9A0M1)
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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9A0M1_STRP1 | Q9A0M1: 2xgr

(-) Related Entries Specified in the PDB File

2xgr EXTRACELLULAR ENDONUCLEASE