2NQ9 - JenaLib

Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV (ENDO IV) Y72A MUTANT BOUND TO DAMAGED DNA

Authors :   E. D. Garcin-Hosfield, D. J. Hosfield, J. A. Tainer

Date :   30 Oct 06 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Tim-Barrel, Trinuclear Zn Active Site, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. D. Garcin, D. J. Hosfield, S. A. Desai, B. J. Haas, M. Bjoras, R. P. Cunningham, J. A. Tainer
Dna Apurinic-Apyrimidinic Site Binding And Excision By Endonuclease Iv.
Nat. Struct. Mol. Biol. V. 15 515 2008
PubMed-ID: 18408731 | Reference-DOI: 10.1038/NSMB.1414
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'-D(APTPAPTPCPT)-3'*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(P(3DR)PAPGPAPT)-3'**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(APTPCPTPGPAPAPGPTPAPT)-3'**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - ENDONUCLEASE 4
	Chains	:	A
	EC Number	:	3.1.21.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24
	Expression System Strain	:	NFO- STRAIN BW565DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NFO
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ENDONUCLEASE IV, ENDODEOXYRIBONUCLEASE IV

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 4)

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
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Chain A from PDB  Type:PROTEIN  Length:279
 aligned with END4_ECOLI | P0A6C1 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
           END4_ECOLI     1 MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQ 279
               SCOP domains d2nq9a_ A: Endonuclease IV                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2nq9A00 A:1-279 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------AP_endonuc_2-2nq9A01 A:19-239                                                                                                                                                                                                ---------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhh.hhh.eeeeeehhhhhhh.....hhhhhhhhhhhhhhhhhhh.eeeeee.ee..........ee.......hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AP_NUCLEASE_F2_4  PDB: A:1-279 UniProt: 1-280                                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------AP_NUCLEA-------------------------------------------------------------------------------------------------AP_NUCLE--------------------------------AP_NUCLEASE_F2_3 ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nq9 A   1 MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSALINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQ 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:DNA  Length:6
                                      
                 2nq9 B 301 ATATCT 306

Chain C from PDB  Type:DNA  Length:5
                                     
                 2nq9 C 307 xAGAT 311
                            |    
                          307-3DR

Chain D from PDB  Type:DNA  Length:11
                                           
                 2nq9 D 335 ATCTGAAGTAT 345
                                   344

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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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (END4_ECOLI | P0A6C1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003906	DNA-(apurinic or apyrimidinic site) lyase activity	Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
	GO:0008833	deoxyribonuclease IV (phage-T4-induced) activity	Catalysis of the endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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: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.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	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:0000726	non-recombinational repair	A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA.
	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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