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(-) Description

Title :  RADA RECOMBINASE FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH AMPPNP
 
Authors :  Y. Li, Y. He, Y. Luo
Date :  08 Oct 08  (Deposition) - 05 May 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Rada, Strand Exchange Protein, Atpase, Recombinase, Atp Analogue, Atp-Binding, Dna Damage, Dna Recombination, Dna- Binding, Nucleotide-Binding, Dna Binding Protein, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, Y. He, Y. Luo
Conservation Of A Conformational Switch In Rada Recombinase From Methanococcus Maripaludis.
Acta Crystallogr. , Sect. D V. 65 602 2009
PubMed-ID: 19465774  |  Reference-DOI: 10.1107/S0907444909011871
(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 Plasmid: PET28A
    Expression System Strain: BL21-ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MMP1222, RADA
    Mutation: YES
    Organism Scientific: METHANOCOCCUS MARIPALUDIS
    Organism Taxid: 39152

 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
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE 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 , GLN A:257 , TYR A:301 , ASP 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:602 , HOH A:608BINDING 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

(-) SS Bonds  (0, 0)

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

(-) 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 3ETL)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECA_2PS50162 RecA family profile 1.RADA_METMI76-258  1A:76-258
RADA_METMP76-258  1A:76-258
2RECA_3PS50163 RecA family profile 2.RADA_METMI263-322  1A:279-322
RADA_METMP263-322  1A:279-322

(-) Exons   (0, 0)

(no "Exon" information available for 3ETL)

(-) 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:302
 aligned with RADA_METMI | P0CW58 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:321
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321 
           RADA_METMI     2 ADVLTELPGVGPSTADKLIEGGYLDFMKIATATIGELTDIEGISEKAAAKMIMAARDLCDLGFKSGVELLKQRQSVWRLSTGSTELGTVLAGGIESQSVTEFAGMFGSGKTQIMHQTCVNLQMREKIFADLEGVVEEELEAPKAVYIDTEGTFRPERVVQMAEGAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIKGGNNIKLVIIDSLTSTFRNEFTGRGKLAERQQKLGRHMATLNKLADLYNCIVLVTNQVAAKPDAYFGVAEQAIGGHVVGHAATFRFFLRKSKGDKRVAKLYDSPHLPDSEAVFRITEKGIQD 322
               SCOP domains d3etla1 A:2-63 automated matches                              d3etla2 A:64-322 automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhh...ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhhh....ee......hhhhh..eeeeeee.....hhhhhhhhhhhhh.hhhhhhhheeeee..hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..-------------------.....eeeeeee....eeeeeeee......eeeeeee....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------RECA_2  PDB: A:76-258 UniProt: 76-258                                                                                                                                                  ---------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RECA_3  PDB: A:279-322 UniProt: 263-322                      PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3etl A   2 ADVLTELPGVGPSTADKLIEGGYLDFMKIATATIGELTDIEGISEKAAAKMIMAARDLCDLGFKSGVELLKQRQSVWRLSTGSTELDTVLAGGIESQSVTEFAGMFGSGKTQIMHQTCVNLQMREKIFADLEGVVEEELEAPKAVYIDTEGTFRPERVVQMAEGAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIKGGNNIKLVIIDSLTSTFRNEFTGRGKLAERQQKLGRHMATLNKLADLYNCIVLVTNQVA-------------------GHAATFRFFLRKSKGDKRVAKLYDSPHLPDSEAVFRITEKGIQD 322
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -         -       281       291       301       311       321 
                                                                                                                                                                                                                                                                                           259                 279                                           


Chain A from PDB  Type:PROTEIN  Length:302
 aligned with RADA_METMP | P0CW59 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:321
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321 
           RADA_METMP     2 ADVLTELPGVGPSTADKLIEGGYLDFMKIATATIGELTDIEGISEKAAAKMIMAARDLCDLGFKSGVELLKQRQSVWRLSTGSTELDTVLAGGIESQSVTEFAGMFGSGKTQIMHQTCVNLQIREKIFADLEGVVEEELEAPKAVYIDTEGTFRPERVVQMAEGAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIKGGNNIKLVIIDSLTSTFRNEFTGRGKLAERQQKLGRHMATLNKLADLYNCIVLVTNQVAAKPDAYFGVAEQAIGGHVVGHAATFRFFLRKSKGDKRVAKLYDSPHLPDSEAVFRITEKGIQD 322
               SCOP domains d3etla1 A:2-63 automated matches                              d3etla2 A:64-322 automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhh...ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhhh....ee......hhhhh..eeeeeee.....hhhhhhhhhhhhh.hhhhhhhheeeee..hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..-------------------.....eeeeeee....eeeeeeee......eeeeeee....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------RECA_2  PDB: A:76-258 UniProt: 76-258                                                                                                                                                  ---------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RECA_3  PDB: A:279-322 UniProt: 263-322                      PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3etl A   2 ADVLTELPGVGPSTADKLIEGGYLDFMKIATATIGELTDIEGISEKAAAKMIMAARDLCDLGFKSGVELLKQRQSVWRLSTGSTELDTVLAGGIESQSVTEFAGMFGSGKTQIMHQTCVNLQMREKIFADLEGVVEEELEAPKAVYIDTEGTFRPERVVQMAEGAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIKGGNNIKLVIIDSLTSTFRNEFTGRGKLAERQQKLGRHMATLNKLADLYNCIVLVTNQVA-------------------GHAATFRFFLRKSKGDKRVAKLYDSPHLPDSEAVFRITEKGIQD 322
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -         -       281       291       301       311       321 
                                                                                                                                                                                                                                                                                           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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RADA_METMI | P0CW58)
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.

Chain A   (RADA_METMP | P0CW59)
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)

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        RADA_METMI | P0CW58: 3ew9 3ewa
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(-) Related Entries Specified in the PDB File

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