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(-) Description

Title :  RECOMBINASE IN COMPLEX WITH ADP
 
Authors :  X. Qian, Y. He, Y. Wu, Y. Luo
Date :  14 Nov 05  (Deposition) - 30 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Atpase, Protein-Atp Complex, Rad51, Reca, Recombinase, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qian, Y. He, Y. Wu, Y. Luo
Asp302 Determines Potassium Dependence Of A Rada Recombinase From Methanococcus Voltae.
J. Mol. Biol. V. 360 537 2006
PubMed-ID: 16782126  |  Reference-DOI: 10.1016/J.JMB.2006.05.058
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 562
    Gene: RADA
    Mutation: YES
    Organism Scientific: METHANOCOCCUS VOLTAE
    Organism Taxid: 2188

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:112 , ADP A:401 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:608BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLN A:98 , ASP A:246 , HOH A:604 , HOH A:605 , HOH A:606 , HOH A:607BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREPHE A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , GLN A:113 , ARG A:158 , GLN A:161 , ARG A:296 , TYR A:301 , ASP A:302 , SER A:303 , PRO A:304 , HIS A:305 , LEU A:306 , ASP A:308 , THR A:316 , GLU A:317 , MG A:501 , HOH A:602 , HOH A:608 , HOH A:630 , HOH A:642BINDING SITE FOR RESIDUE ADP A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F1J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:211 -Ser A:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F1J)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECA_2PS50162 RecA family profile 1.RADA_METVO76-258  1A:76-258
2RECA_3PS50163 RecA family profile 2.RADA_METVO263-322  1A:279-322

(-) Exons   (0, 0)

(no "Exon" information available for 2F1J)

(-) 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:299
 aligned with RADA_METVO | O73948 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:318
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314        
           RADA_METVO     5 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLGFKSGIDLLKQRSTVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVSAKPDAFFGMAEQAIGGHIVGHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGIQD 322
               SCOP domains d2f1ja1 A:5-63 automated matches                           d2f1ja2 A:64-322 automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2f1jA01 A:5-66 5' to 3' exonuclease, C-terminal subdomain     2f1jA02 A:67-322 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhh..ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhhhhhh.ee......hhhhhh..eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..-------------------.....eeeeeee....eeeeeeee......eeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------RECA_2  PDB: A:76-258 UniProt: 76-258                                                                                                                                                  ----RECA_3  PDB: A:279-322 UniProt: 263-322                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f1j A   5 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLGFKSGIDLLKQRSTVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTDGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVS-------------------GHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGIQD 322
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    |    -         -    |  284       294       304       314        
                                                                                                                                                                                                                                                                                        259                 279
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F1J)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RADA_METVO | O73948)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RADA_METVO | O73948: 1t4g 1xu4 2b21 2f1h 2f1i 2fpk 2fpl 2fpm 2gdj 2i1q 3fyh 3ntu 4dc9 4qkq

(-) Related Entries Specified in the PDB File

2f1h THE SAME MUTANT PROTEIN COMPLEXED WITH ADP
2f1i THE SAME MUTANT PROTEIN COMPLEXED WITH ADP