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(-) Description

Title :  POTASSIUM BOUND STRUCTURE OF E. COLI EXOIX IN P1
 
Authors :  C. S. Anstey-Gilbert, G. R. Hemsworth, C. S. Flemming, M. R. G. Hodskins J. Zhang, S. E. Sedelnikova, T. J. Stillman, J. R. Sayers, P. J. Artymiu
Date :  26 Nov 12  (Deposition) - 10 Jul 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Flap Endonuclease, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. S. Anstey-Gilbert, G. R. Hemsworth, C. S. Flemming, M. R. G. Hodskinson, J. Zhang, S. E. Sedelnikova, T. J. Stillman, J. R. Sayers, P. J. Artymiuk
The Structure Of E. Coli Exoix - Implications For Dna Binding And Catalysis In Flap Endonucleases
Nucleic Acids Res. V. 41 8357 2013
PubMed-ID: 23821668  |  Reference-DOI: 10.1093/NAR/GKT591

(-) Compounds

Molecule 1 - PROTEIN XNI
    ChainsA, B
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantPCI857
    Expression System VectorPJONEX
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainXL1 BLUE
    SynonymEXOIX

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:171 , ALA B:172 , PRO B:180 , VAL B:182 , ILE B:185BINDING SITE FOR RESIDUE K B1251
2AC2SOFTWARELEU A:171 , ALA A:172 , PRO A:180 , VAL A:182 , ILE A:185 , HOH A:2095 , HOH B:2012BINDING SITE FOR RESIDUE K A1252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZD8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:23 -Pro A:24
2Ser B:23 -Pro B:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZD8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZD8)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZD8)

(-) 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:239
 aligned with XNI_ECO57 | Q8X6R9 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:250
                                    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
            XNI_ECO57     2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLVR 251
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeee..------hhhhhhh..........hhhhhhhhhhhhhhhhhh...ee.-----hhhhhhhhhhhhhhh..eeeee..hhhhhhhh...eeeee....ee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zd8 A   2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFD------GWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWS-----ADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLVR 251
                                    11        21        31        41        |-     |  61        71        81        91     |   - |     111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
                                                                           50     57                                      97   103                                                                                                                                                    

Chain A from PDB  Type:PROTEIN  Length:239
 aligned with XNI_ECOLI | P38506 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:250
                                    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
            XNI_ECOLI     2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLVR 251
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeee..------hhhhhhh..........hhhhhhhhhhhhhhhhhh...ee.-----hhhhhhhhhhhhhhh..eeeee..hhhhhhhh...eeeee....ee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zd8 A   2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFD------GWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWS-----ADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLVR 251
                                    11        21        31        41        |-     |  61        71        81        91     |   - |     111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
                                                                           50     57                                      97   103                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with XNI_ECO57 | Q8X6R9 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
            XNI_ECO57     2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeee...-----hhhhhhh..........hhhhhhhhhhhhhhhhhh...ee.-----hhhhhhhhhhhhhhh..eeeee..hhhhhhhh...eeeee....ee.hhhhhhhhh..hhhhhhhhhhhhh.hhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zd8 B   2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDD-----GWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWS-----ADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
                                    11        21        31        41        51     |  61        71        81        91     |   - |     111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                                            51    57                                      97   103                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with XNI_ECOLI | P38506 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
            XNI_ECOLI     2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWSTSGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeee...-----hhhhhhh..........hhhhhhhhhhhhhhhhhh...ee.-----hhhhhhhhhhhhhhh..eeeee..hhhhhhhh...eeeee....ee.hhhhhhhhh..hhhhhhhhhhhhh.hhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zd8 B   2 AVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIMHSQPTHAVAVFDD-----GWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWS-----ADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEFGVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKLETHKEMAFLCRDIARLQTDLHIDGNLQQLRLV 250
                                    11        21        31        41        51     |  61        71        81        91     |   - |     111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                                            51    57                                      97   103                                                                                                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 3ZD8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZD8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZD8)

(-) Gene Ontology  (16, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XNI_ECO57 | Q8X6R9)
molecular function
    GO:0017108    5'-flap endonuclease activity    Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0048256    flap endonuclease activity    Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
biological process
    GO:0033567    DNA replication, Okazaki fragment processing    The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Chain A,B   (XNI_ECOLI | P38506)
molecular function
    GO:0008409    5'-3' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
    GO:0017108    5'-flap endonuclease activity    Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0048256    flap endonuclease activity    Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0033567    DNA replication, Okazaki fragment processing    The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XNI_ECO57 | Q8X6R93zd9 3zda 3zdb 3zdc 3zdd 3zde
        XNI_ECOLI | P385063zd9 3zda 3zdb 3zdc 3zdd 3zde

(-) Related Entries Specified in the PDB File

3zd9 POTASSIUM BOUND STRUCTURE OF E. COLI EXOIX IN P21
3zda STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH A FRAGMENT OF THE FLAP1 DNA OLIGOCULEOTIDE, POTASSIUM AND MAGNESIUM
3zdb STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA OLIGONUCLEOTIDE, DI-MAGNESIUM AND POTASSIUM
3zdc STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV4 DNA OLIGONUCLEOTIDE, POTASSIUM AND CALCIUM
3zdd STRUCTURE OF E. COLI EXOIX IN COMPLEX WITH THE PALINDROMIC 5OV6 OLIGONUCLEOTIDE AND POTASSIUM
3zde POTASSIUM FREE STRUCTURE OF E. COLI EXOIX