2FPL - JenaLib

Title :   RADA RECOMBINASE IN COMPLEX WITH AMP-PNP AND LOW CONCENTRATION OF K+

Authors :   Y. Wu, X. Qian, Y. He, I. A. Moya, Y. Luo

Date :   16 Jan 06 (Deposition) - 31 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Atpase, Protein-Atp Complex, Rada/Adp Complex, Co-Factors, Potassium-Dependence, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Qian, Y. Wu, Y. He, I. A. Moya, Y. Luo
Crystal Structure Of Methanococcus Voltae Rada In Complex With Adp: Hydrolysis-Induced Conformational Change
Biochemistry V. 44 13753 2005
PubMed-ID: 16229465 | Reference-DOI: 10.1021/BI051222I
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:112 , ANP A:401 , HOH A:601 , HOH A:602 , HOH A:603	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	GLN A:98 , ASP A:246 , HOH A:604 , HOH A:605 , HOH A:606 , HOH A:607	BINDING SITE FOR RESIDUE MG A 502
3	AC3	SOFTWARE	ALA A:282 , THR A:283 , ASP A:302 , ANP A:401 , HOH A:608 , HOH A:660	BINDING SITE FOR RESIDUE K A 503
4	AC4	SOFTWARE	TYR A:301 , ASP A:308 , ANP A:401 , HOH A:632	BINDING SITE FOR RESIDUE K A 505
5	AC5	SOFTWARE	THR A:6 , LEU A:8 , VAL A:11 , GLU A:164 , HOH A:691 , HOH A:720	BINDING SITE FOR RESIDUE K A 506
6	AC6	SOFTWARE	PHE 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 , 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 , K A:503 , K A:505 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:608 , HOH A:621 , HOH A:623 , HOH A:629 , HOH A:632 , HOH A:638 , HOH A:639 , HOH A:660	BINDING SITE FOR RESIDUE ANP A 401

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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 d2fpla1 A:5-64 DNA repair protein Rad51, N-terminal domain  d2fpla2 A:65-322 DNA repair protein Rad51, catalytic domain                                                                                                                                                                                                        SCOP domains
               CATH domains 2fplA01 A:5-66 5' to 3' exonuclease, C-terminal subdomain     2fplA02 A:67-322 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhh...ee...hhhhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhh.ee.......hhhhh..eeeeee.....hhhhhhhhhhh...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
                 2fpl A   5 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLGFKSGIDLLKQRSTVWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVS-------------------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)

CATH Domains (2, 2)

Pfam Domains (0, 0)

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. Interchromosomal 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:211 - Ser A:212	[ RasMol ]

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