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(-) Description

Title :  RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS
 
Authors :  M. E. Marsh, M. T. Ehebauer, D. Scott, C. Abell, T. L. Blundell, M. Hyvone
Date :  08 Nov 11  (Deposition) - 14 Nov 12  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Recombinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Marsh, D. E. Scott, M. T. Ehebauer, C. Abell, T. L. Blundell, M. Hyvonen
Atp Half-Sites In Rada And Rad51 Recombinases Bind Nucleotides
Febs Open Bio V. 6 372 2016
PubMed-ID: 27419043  |  Reference-DOI: 10.1002/2211-5463.12052

(-) Compounds

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAT
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL ATPASE DOMAIN, RESIDUES 108-288 AND 301-349
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: RADA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:140 , GLY A:141 , SER A:142 , GLY A:143 , LYS A:144 , THR A:145 , HOH A:2064 , HOH A:2065 , HOH A:2071 , HOH A:2431 , HOH A:2432BINDING SITE FOR RESIDUE PO4 A1350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A6P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:238 -Ser A:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A6P)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECA_2PS50162 RecA family profile 1.RADA_PYRFU109-285  1A:109-285
2RECA_3PS50163 RecA family profile 2.RADA_PYRFU290-349  1A:304-349

(-) Exons   (0, 0)

(no "Exon" information available for 4A6P)

(-) 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    
   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:219
 aligned with RADA_PYRFU | O74036 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:242
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
           RADA_PYRFU   108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPDAFFGDPTRPIGGHILAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED 349
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhh..hhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.------------------.......eeeeeee.--.eeeeeee..---....eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RECA_2  PDB: A:109-285 UniProt: 109-285                                                                                                                                          ----RECA_3  PDB: A:304-349 UniProt: 290-349                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a6p A 108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQV------------------ILAHSATLRVYLRKG--GKRIARLIDA---PEGEAVFSITEKGIED 349
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       | -         -      |307       317|  |   327  |   |337       347  
                                                                                                                                                                                                           285                304           318  |      330 334               
                                                                                                                                                                                                                                               321
   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 4A6P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A6P)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RADA_PYRFU | O74036)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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  RADA_PYRFU | O74036
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 Related Entries

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

UniProtKB/Swiss-Prot
        RADA_PYRFU | O74036: 1pzn 4a6x 4b2i 4b2l 4b2p 4b32 4b33 4b34 4b35 4b3b 4b3c 4b3d 4d6p 4uqo 5fos 5fot 5fou 5fov 5fow 5fox 5fpk 5j4h 5j4k 5j4l 5jec 5jed 5jee 5jfg 5kdd 5l8v 5lb2 5lb4 5lbi

(-) Related Entries Specified in the PDB File

1pzn RAD51 (RADA)