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(-) Description

Title :  RADA RECOMBINASE D302K MUTANT IN COMPLEX WITH AMP-PNP
 
Authors :  Y. Luo
Date :  05 Jul 10  (Deposition) - 27 Jul 11  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Atpase, Recombinase, Atp Complex, Active Conformation, Reca, Rad51, Dmc1, Rada, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Amunugama, Y. He, S. Willcox, R. A. Forties, K. S. Shim, R. Bundschuh Y. Luo, J. Griffith, R. Fishel
Rad51 Protein Atp Cap Regulates Nucleoprotein Filament Stability.
J. Biol. Chem. V. 287 8724 2012
PubMed-ID: 22275364  |  Reference-DOI: 10.1074/JBC.M111.239426

(-) Compounds

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21-CODONPLUS-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 4-322
    GeneRADA
    MutationYES
    Organism ScientificMETHANOCOCCUS VOLTAE
    Organism Taxid523842
    StrainDSM 1537 / PS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (6x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ANP6Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , GLN A:113 , GLU A:151 , ARG A:158 , GLN A:161 , HIS A:280 , ARG A:296 , LYS A:302 , SER A:303 , PRO A:304 , HIS A:305 , LEU A:306 , PRO A:307 , ASP A:308 , THR A:316 , GLU A:317 , MG A:501 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:609 , HOH A:617 , HOH A:623 , HOH A:641 , HOH A:660 , HOH A:662 , HOH A:691BINDING SITE FOR RESIDUE ANP A 401
2AC2SOFTWARETHR A:112 , ANP A:401 , HOH A:601 , HOH A:602 , HOH A:603BINDING SITE FOR RESIDUE MG A 501
3AC3SOFTWAREGLN A:98 , ASP A:246 , HOH A:604 , HOH A:605 , HOH A:606 , HOH A:607BINDING SITE FOR RESIDUE MG A 502
4AC4SOFTWARETHR A:6 , LEU A:8 , VAL A:11 , GLU A:164BINDING SITE FOR RESIDUE NA A 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric 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:269-322
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECA_2PS50162 RecA family profile 1.RADA_METVO76-258  6A:76-258
2RECA_3PS50163 RecA family profile 2.RADA_METVO263-322  6A:269-322

(-) Exons   (0, 0)

(no "Exon" information available for 3NTU)

(-) 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    
   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:310
 aligned with RADA_METVO | O73948 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:319
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313         
           RADA_METVO     4 NLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLGFKSGIDLLKQRSTVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVSAKPDAFFGMAEQAIGGHIVGHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGIQD 322
               SCOP domains d3ntua1 A:4-63 DNA repair protein Rad51, N-terminal domain  d3ntua2 A:64-322 DNA repair protein Rad51, catalytic domain                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhh...ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhhhhhh.ee.............eeeeeee.....hhhhhhhhhhhhh.hhhhhhhheeeee..hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhh.--...hhhhhhhhhhhhhhhhhhhhh..eeeeee.ee..-------..ee.hhhhhhhhh.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:269-322 UniProt: 263-322                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ntu A   4 GLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLGFKSGIDLLKQRSTVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYT--GKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVSAK-------AEQAIGGHIVGHAATFRFFVRKGKGDKRVAKLYKSPHLPDAEAIFRITEKGIQD 322
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        |- |     233       243       253       | -     | 273       283       293       303       313         
                                                                                                                                                                                                                                                    222  |                                 261     269                                                     
                                                                                                                                                                                                                                                       225                                                                                                 

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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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric 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 | O739481t4g 1xu4 2b21 2f1h 2f1i 2f1j 2fpk 2fpl 2fpm 2gdj 2i1q 3fyh 4dc9 4qkq

(-) Related Entries Specified in the PDB File

1t4g WILD-TYPE PROTEIN IN COMPLEX WITH AMP-PNP
2i1q WILD-TYPE PROTEIN IN COMPLEX WITH AMP-PNP AND CALCIUM