2JC5 - JenaLib

Title :   APURINIC APYRIMIDINIC (AP) ENDONUCLEASE (NAPE) FROM NEISSERIA MENINGITIDIS

Authors :   E. P. Carpenter, A. Corbett, H. Thomson, J. Adacha, K. Jensen, J. Bergeron, I. Kasampalidis, R. Exley, M. Winterbotham, C. Tang, G. S. Baldwin, P. Freemont

Date :   19 Dec 06 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Neisseria Meningitidis, Repair Phosphodiesterase, Dna Repair, Exonuclease, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. P. Carpenter, A. Corbett, H. Thomson, J. Adacha, K. Jensen, J. Bergeron, I. Kasampalidis, R. Exley, M. Winterbotham, C. Tang, G. S. Baldwin, P. Freemont
Ap Endonuclease Paralogues With Distinct Activities In Dna Repair And Bacterial Pathogenesis.
Embo J. V. 26 1363 2007
PubMed-ID: 17318183 | Reference-DOI: 10.1038/SJ.EMBOJ.7601593

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , GLU A:36 , HOH A:2043 , HOH A:2045 , HOH A:2291 , HOH A:2292	BINDING SITE FOR RESIDUE MG A1260
2	AC2	SOFTWARE	SER A:112 , GLY A:113 , SER A:114 , LYS A:123 , ASN A:151 , SER A:169 , GLU A:228 , HOH A:2303	BINDING SITE FOR RESIDUE BCN A1261
3	AC3	SOFTWARE	TYR A:124 , GLU A:174 , HOH A:2311	BINDING SITE FOR RESIDUE DIO A1264
4	AC4	SOFTWARE	TYR A:16 , TYR A:21 , ASP A:47 , HOH A:2062 , HOH A:2312 , HOH A:2313	BINDING SITE FOR RESIDUE DIO A1265
5	AC5	SOFTWARE	ASP A:30 , ILE A:31 , LYS A:74 , ARG A:75 , PHE A:100 , ALA A:258 , HOH A:2037 , HOH A:2306 , HOH A:2307	BINDING SITE FOR RESIDUE GOL A1262
6	AC6	SOFTWARE	TYR A:212 , ASP A:215 , LYS A:240 , HOH A:2281 , HOH A:2309 , HOH A:2310	BINDING SITE FOR RESIDUE GOL A1263

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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:259
 aligned with Q7DD47_NEIMB | Q7DD47 from UniProtKB/TrEMBL  Length:259

    Alignment length:259
                                    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         
         Q7DD47_NEIMB     1 MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDYAAE 259
               SCOP domains d2jc5a_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Exo_endo_phos-2jc5A01 A:5-247                                                                                                                                                                                                                      ------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhheeeee.........eeeee.....eeee...hhhhhh...eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhh.............hhhhhhhhhhhhhh...eehhhhhh.......ee...hhhhhh..ee..eeeeehhhhhh.eeeeee...........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jc5 A   1 MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVEYDYAAE 259
                                    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

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q7DD47_NEIMB | Q7DD47)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0008853	exodeoxyribonuclease III activity	Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides.
	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: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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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