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(-) Description

Title :  STRUCTURES OF ARCHAEAL MEMBERS OF THE LIGD 3'-PHOSPHOESTERASE DNA REPAIR ENZYME SUPERFAMILY
 
Authors :  P. Smith, P. A. Nair, U. Das, H. Zhu, S. Shuman
Date :  06 Oct 10  (Deposition) - 19 Jan 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphoesterase, Metalloenzyme, Manganese, Beta Barrel, Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Smith, P. A. Nair, U. Das, H. Zhu, S. Shuman
Structures And Activities Of Archaeal Members Of The Ligd 3'-Phosphoesterase Dna Repair Enzyme Superfamily.
Nucleic Acids Res. V. 39 3310 2011
PubMed-ID: 21208981  |  Reference-DOI: 10.1093/NAR/GKQ1163

(-) Compounds

Molecule 1 - ATP-DEPENDENT DNA LIGASE, N-TERMINAL DOMAIN PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28BSMT3HIS10
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KCR_0736
    Organism Scientific: CANDIDATUS KORARCHAEUM CRYPTOFILUM
    Organism Taxid: 374847
    Strain: OPF8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , HIS A:15 , ASP A:17 , PO4 A:119 , HOH A:247 , HOH A:249BINDING SITE FOR RESIDUE MN A 118
2AC2SOFTWAREHIS A:9 , ASP A:17 , ARG A:19 , HIS A:51 , GLY A:68 , MN A:118 , PEG A:120 , HOH A:227 , HOH A:247 , HOH A:249 , HOH A:250 , HOH A:310BINDING SITE FOR RESIDUE PO4 A 119
3AC3SOFTWAREHIS A:15 , ALA A:30 , THR A:48 , GLU A:49 , ARG A:97 , PO4 A:119 , HOH A:145 , HOH A:192 , HOH A:200 , HOH A:247 , HOH A:312 , HOH A:315BINDING SITE FOR RESIDUE PEG A 120

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P4H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P4H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P4H)

(-) Exons   (0, 0)

(no "Exon" information available for 3P4H)

(-) 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    
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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:118
 aligned with B1L4V6_KORCO | B1L4V6 from UniProtKB/TrEMBL  Length:117

    Alignment length:118
                             1                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109        
         B1L4V6_KORCO     - -MPRFVVQEHHARRLHWDLRLEMDNVLKSWALPKGVPEKRGVKRLAIETEDHDLSYIDFEGRIPEGMYGAGEVKIWDSGEYELLERTENKIKFLAKGRKMNGEYVLIKTKVGWLLMKA 117
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------LigD_N-3p4hA01 A:7-107                                                                               ---------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeeee..eeeeeee..........eeeeeeeeeehhhhhhh.eee.......eeeeeeeeeeeeeeeee..eeeeeee....eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3p4h A   0 SMPRFVVQEHHARRLHWDLRLEMDNVLKSWALPKGVPEKRGVKRLAIETEDHDLSYIDFEGRIPEGMYGAGEVKIWDSGEYELLERTENKIKFLAKGRKMNGEYVLIKTKVGWLLMKA 117
                                     9        19        29        39        49        59        69        79        89        99       109
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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 3P4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P4H)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: LigD_N] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B1L4V6_KORCO | B1L4V6)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/TrEMBL
        B1L4V6_KORCO | B1L4V6: 3ta5 3ta7

(-) Related Entries Specified in the PDB File

3p43