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(-) Description

Title :  RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO GTP
 
Authors :  M. E. Marsh, M. T. Ehebauer, D. Scott, C. Abell, T. L. Blundell, M. Hyvone
Date :  17 Jul 12  (Deposition) - 24 Jul 13  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (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 108-349
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:140 , GLY A:141 , SER A:142 , GLY A:143 , LYS A:144 , THR A:145 , GLN A:146 , ARG A:181 , GLN A:284 , ARG A:323 , ILE A:342 , MG A:1351 , GOL A:1353 , HOH A:2022 , HOH A:2023 , HOH A:2024 , HOH A:2025 , HOH A:2044 , HOH A:2053 , HOH A:2054 , HOH A:2108 , HOH A:2117BINDING SITE FOR RESIDUE GTP A1350
2AC2SOFTWARETHR A:145 , GTP A:1350 , HOH A:2023 , HOH A:2024 , HOH A:2025BINDING SITE FOR RESIDUE MG A1351
3AC3SOFTWAREILE A:169 , LEU A:214 , ALA A:218 , HOH A:2073BINDING SITE FOR RESIDUE GOL A1352
4AC4SOFTWARETHR A:145 , GLN A:146 , HIS A:149 , THR A:176 , ARG A:178 , GTP A:1350 , HOH A:2026BINDING SITE FOR RESIDUE GOL A1353

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B2P)

(-) 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 4B2P)

(-) 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 4B2P)

(-) 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:216
 aligned with RADA_PYRFU | O74036 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:241
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348 
           RADA_PYRFU   109 TIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPDAFFGDPTRPIGGHILAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...hhhhhhhhh..ee..eeeeeee....hhhhhhhhhhhhh..hhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh.eeeeeee.------------------.......eeeeeee.hhh.eeeeee-------..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
                 4b2p A 109 TIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQV------------------ILAHSATLRVYLRKGKGGKRIARLI-------GEAVFSITEKGIED 349
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      |  -         -     | 308       318       328       338       348 
                                                                                                                                                                                                          285                304                     328     336
   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 4B2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B2P)

(-) 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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    Asp A:238 - Ser A:239   [ RasMol ]  
 

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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 4a6p 4a6x 4b2i 4b2l 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)
4a6p RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS
4a6x RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ATP
4a74 RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO AMPPNP
4a7o RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP
4b2i HUMANISED MONOMERIC RADA IN COMPLEX WITH INDAZOLE
4b2l HUMANISED MONOMERIC RADA IN COMPLEX WITH L-METHYLESTER TRYPTOPHAN