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(-) Description

Title :  CRYSTAL STRUCTURE OF LHK-EXO IN COMPLEX WITH 5-PHOSPHORYLATED OLIGOTHYMIDINE (DT)4
 
Authors :  W. Yang, W. Y. Chen, H. Wang, Q. Zhang, W. Zhou, M. Bartlam, R. M. Watt, Z. R
Date :  18 Jul 11  (Deposition) - 15 Feb 12  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Alkaline Exonuclease, Digest Double Stranded Dna, Strict 5-3- Polarity, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Yang, W. Y. Chen, H. Wang, J. W. Ho, J. D. Huang, P. C. Woo, S. K. Lau, K. Y. Yuen, Q. Zhang, W. Zhou, M. Bartlam, R. M. Watt, Z. Rao
Structural And Functional Insight Into The Mechanism Of An Alkaline Exonuclease From Laribacter Hongkongensis.
Nucleic Acids Res. V. 39 9803 2011
PubMed-ID: 21893587  |  Reference-DOI: 10.1093/NAR/GKR660

(-) Compounds

Molecule 1 - EXONUCLEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LHK_01497
    Organism Scientific: LARIBACTER HONGKONGENSIS
    Organism Taxid: 557598
    Strain: HLHK9
    Synonym: ALKALINE EXONUCLEASE, LHK-EXO
 
Molecule 2 - 5'-D(P*TP*TP*TP*T)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:102 , GLU A:112 , ILE A:113 , DT B:211BINDING SITE FOR RESIDUE MG A 220
2AC2SOFTWARESER A:100 , ASP A:102 , GLU A:112 , DT B:210 , DT B:211BINDING SITE FOR RESIDUE MG A 221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SZ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SZ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SZ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SZ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3SZ5)

(-) 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    
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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:194
 aligned with C1D7P6_LARHH | C1D7P6 from UniProtKB/TrEMBL  Length:203

    Alignment length:202
                                                                                                                                                                                                                                203   
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194        |-  
         C1D7P6_LARHH     5 TEEWFAARLGKVTASRVADVMTKTKSGYAASRQNYMAELICQRLTGTQEIRFSNAAMQRGTELEPHARARYIIETGEIVTEVGLIDHPTIAGFGASPDGLVGDTGLIEIKCPNTWTHIETIKTGKPKPEYIKQMQTQMACTGRQWCDFVSYDDRLPDDMQYFCTRIERDDALIAEIETEVSAFLAELEAEIEYLKRKAA---   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..ee..hhhhhh..-----hhhhhhhhhhhhhhhhhh....---hhhhhhhhhhhhhhhhhhhhhhh..ee....ee......eee...eee...eeeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeeee....hhhhheeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sz5 A   5 TEEWFAARLGKVTASRVADVMTK-----AASRQNYMAELICQRLTGTQEI---NAAMQRGTELEPHARARYIIETGEIVTEVGLIDHPTIAGFGASPDGLVGDTGLIEIKCPNTWTHIETIKTGKPKPEYIKQMQTQMACTGRQWCDFVSYDDRLPDDMQYFCTRIERDDALIAEIETEVSAFLAELEAEIEYLKRKAAKLA 206
                                    14        24  |     34        44        54   |    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  
                                                 27    33                   54  58                                                                                                                                                    


Chain B from PDB  Type:DNA  Length:4
                                    
                 3sz5 B 210 TTTT 213
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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 3SZ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SZ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SZ5)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (C1D7P6_LARHH | C1D7P6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/TrEMBL
        C1D7P6_LARHH | C1D7P6: 3syy 3sz4

(-) Related Entries Specified in the PDB File

3syy CRYSTAL STRUCTURE OF AN ALKALINE EXONUCLEASE (LHK-EXO) FROM LARIBACTER HONGKONGENSIS
3sz4 CRYSTAL STRUCTURE OF LHK-EXO IN COMPLEX WITH DAMP