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(-) Description

Title :  THE STRUCTURE OF PYROCOCCUS FURIOSUS SFSA IN COMPLEX WITH DNA
 
Authors :  P. J. Baker, F. L. Allen
Date :  13 Jan 12  (Deposition) - 01 Oct 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,D,X
Biol. Unit 1:  A (1x),D (2x),X (1x)
Biol. Unit 2:  B (1x),D (1x),X (2x)
Keywords :  Ob Fold, Pd-(D/E)Xk Domain, Nuclease, Protein-Dna Complex, Hydrolase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. L. Allen, J. Akerboom, S. J. Bliss, F. Blombach, S. E. Sedelnikova, J. Van Der Oost, P. J. Baker
The Structure Of Sfsa And Its Dna Complex; A Dna/Rna Nuclease With A Novel Domain Combination
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR FERMENTATION STIMULATION PROTEIN HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SFSA, PF1198
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
 
Molecule 2 - 5'-D(*CP*GP*CP*TP*GP*TP*CP*TP*CP*GP*CP*T)-3'
    Chains: X, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDX
Biological Unit 1 (2x): A (1x) D (2x)X (1x)
Biological Unit 2 (2x):  B (1x)D (1x)X (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4DAV)

(-) Sites  (0, 0)

(no "Site" information available for 4DAV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DAV)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:144 -Pro A:145
3Ser B:7 -Pro B:8
4Tyr B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DAV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DAV)

(-) Exons   (0, 0)

(no "Exon" information available for 4DAV)

(-) 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:231
 aligned with SFSA_PYRFU | Q8U1K8 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:231
                             1                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           SFSA_PYRFU     - -MKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLLECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeeeeeeee..eeeeee..eeeeee...............eeeeee.......eeeeeeee..eeee.hhhhhhhhhhhhhhhh.hhhhh..eeeee..ee..ee..eeee....eeeeeeee..eee..eeee....hhhhhhhhhhhhhhhhh...eeeeeee......eeee....hhhhhhhhhhhhhh..eeeeeeeee....eeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dav A   0 AMKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLIECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with SFSA_PYRFU | Q8U1K8 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:231
                             1                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           SFSA_PYRFU     - -MKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLLECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeeeeeeee..eeeeee..eeeeee...............eeeeee.......eeeeeeee..eeee.hhhhhhhhhhhhhhhh........eeeee..ee..ee..eeee....eeeeeeee..eee..eeee....hhhhhhhhhhhhhhhhh..eeeeeeee......eeee....hhhhhhhhhhhhhhh.eeeeeeeee....eeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dav B   0 AMKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLIECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 


Chain D from PDB  Type:DNA  Length:12
                                            
                 4dav D   1 CGCTGTCTCGCT  12
                                    10  


Chain X from PDB  Type:DNA  Length:12
                                            
                 4dav X   1 CGCTGTCTCGCT  12
                                    10
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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  (0, 0)

(no "SCOP Domain" information available for 4DAV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DAV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DAV)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4DAV)

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  Cis Peptide Bonds
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Tyr A:144 - Pro A:145   [ RasMol ]  
    Tyr B:144 - Pro B:145   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        SFSA_PYRFU | Q8U1K8: 4da2

(-) Related Entries Specified in the PDB File

4da2 PYROCOCCUS FURIOSUS SFSA
4dap E.COLI SFSA