1RXV | PD0501 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A. FULGIDUS FEN-1 BOUND TO DNA

Authors :   B. R. Chapados, D. J. Hosfield, S. Han, J. Qiu, B. Yelent, B. Shen, J. A. Tainer

Date :   18 Dec 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Helical Clamp, Helix-3 Turn-Helix, 3' Flap Binding Site, Protein-Dna Complex, Dna Repair, Dna Replication, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. R. Chapados, D. J. Hosfield, S. Han, J. Qiu, B. Yelent, B. Shen, J. A. Tainer
Structural Basis For Fen-1 Substrate Specificity And Pcna-Mediated Activation In Dna Replication And Repair
Cell(Cambridge, Mass. ) V. 116 39 2004
PubMed-ID: 14718165 | Reference-DOI: 10.1016/S0092-8674(03)01036-5
(for further references see the PDB file header)

*Molecule 1 - 5'-D(TPAPGPCPAPTPCPGPG)**
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SYNTHETIC UPSTREAM PRIMER DNA
	Synthetic	:	YES

Molecule 2 - FLAP STRUCTURE-SPECIFIC ENDONUCLEASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FEN, AF0264
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1RXV)

(no "Site" information available for 1RXV)

(no "SS Bond" information available for 1RXV)

(no "Cis Peptide Bond" information available for 1RXV)

(no "SAP(SNP)/Variant" information available for 1RXV)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XPG_1	PS00841	XPG protein signature 1.	FEN_ARCFU	73-87	2	A:73-87 B:73-87

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XPG_1	PS00841	XPG protein signature 1.	FEN_ARCFU	73-87	1	A:73-87 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XPG_1	PS00841	XPG protein signature 1.	FEN_ARCFU	73-87	1	- B:73-87

(no "Exon" information available for 1RXV)

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:305
 aligned with FEN_ARCFU | O29975 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:320
                                    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       323
            FEN_ARCFU     4 DIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVEEIRNFFLNPPVTDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLK 323
               SCOP domains d1rxva2 A:4-219 Flap endonuclease-1 (Fen-1 nuclease)                                                                                                                                                                    d1rxva1 A:220-323 Flap endonuclease-1 (Fen-1 nuclease)                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..ee.hhhhhh..eeeeehhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh....eee...hhhhhh...eeee....---------------..eeeehhhhhhhhh.hhhhhhhhhhhhee..ee.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------XPG_1          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rxv A   4 DIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAI---------------KPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVEEIRNFFLNPPVTDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLK 323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     |   -         - |     213       223       233       243       253       263       273       283       293       303       313       323
                                                                                                                                                                                                                   189             205

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with FEN_ARCFU | O29975 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:320
                                    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       323
            FEN_ARCFU     4 DIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVEEIRNFFLNPPVTDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLK 323
               SCOP domains d1rxvb2 B:4-219 Flap endonuclease-1 (Fen-1 nuclease)                                                                                                                                                                    d1rxvb1 B:220-323 Flap endonuclease-1 (Fen-1 nuclease)                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---XPG_N-1rxvB03 B:7-101                                                                          -------------------------------------XPG_I-1rxvB01 B:139-235                                                                          ---------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---XPG_N-1rxvB04 B:7-101                                                                          -------------------------------------XPG_I-1rxvB02 B:139-235                                                                          ---------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhh..ee.hhhhhh..eeeeehhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh....eee...hhhhhh...eeee....---------------..eeeehhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhh.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------XPG_1          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rxv B   4 DIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAI---------------KPEIIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDHVEEIRNFFLNPPVTDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLK 323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     |   -         - |     213       223       233       243       253       263       273       283       293       303       313       323
                                                                                                                                                                                                                   189             205

Chain C from PDB  Type:DNA  Length:2
                                  
                 1rxv C   2 GG   1
                            ||
                            2|
                             1

Chain D from PDB  Type:DNA  Length:2
                                  
                 1rxv D   2 GG   1
                            ||
                            ||
                            2|
                             1

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 '\|'

(no "CATH Domain" information available for 1RXV)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FEN_ARCFU | O29975)

molecular function
	GO:0008409	5'-3' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
	GO:0017108	5'-flap endonuclease activity	Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	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:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0043137	DNA replication, removal of RNA primer	Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
	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.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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