2NQJ - JenaLib

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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV (ENDO IV) E261Q MUTANT BOUND TO DAMAGED DNA

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

Date :   31 Oct 06 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Tim_barrel, Trinuclear Zinc Site, Hydrolase (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)

*Molecule 1 - 5'-D(GPCPGPTPCPCP(3DR) PCPGPAPCPGPAPCPG)-3'**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(CPGPTPCPGPTPCPGPGPGPGPAPCPGPC)-3'**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - ENDONUCLEASE 4
	Chains	:	A, B
	EC Number	:	3.1.21.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NFO
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	NFO- STRAIN BW565DE3
	Synonym	:	ENDONUCLEASE IV, ENDODEOXYRIBONUCLEASE IV

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	3DR	-1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:69 , HIS A:109 , GLU A:145 , ZN A:352 , 3DR C:307	BINDING SITE FOR RESIDUE ZN A 351
2	AC2	SOFTWARE	GLU A:145 , ASP A:179 , HIS A:182 , HIS A:216 , GLN A:261 , ZN A:351 , 3DR C:307	BINDING SITE FOR RESIDUE ZN A 352
3	AC3	SOFTWARE	HIS A:182 , ASP A:229 , HIS A:231 , DC C:306 , 3DR C:307	BINDING SITE FOR RESIDUE ZN A 353
4	AC4	SOFTWARE	HIS B:182 , ASP B:229 , HIS B:231 , DG C:315	BINDING SITE FOR RESIDUE ZN B 403

(no "SS Bond" information available for 2NQJ)

(no "Cis Peptide Bond" information available for 2NQJ)

(no "SAP(SNP)/Variant" information available for 2NQJ)

Asymmetric Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AP_NUCLEASE_F2_4	PS51432	AP endonucleases family 2 profile.	END4_ECOLI	1-280	2	A:1-279 B:1-279
2	AP_NUCLEASE_F2_1	PS00729	AP endonucleases family 2 signature 1.	END4_ECOLI	69-77	2	A:69-77 B:69-77
3	AP_NUCLEASE_F2_2	PS00730	AP endonucleases family 2 signature 2.	END4_ECOLI	175-182	2	A:175-182 B:175-182
4	AP_NUCLEASE_F2_3	PS00731	AP endonucleases family 2 signature 3.	END4_ECOLI	215-231	2	A:215-231 B:215-231

Biological Unit 1 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AP_NUCLEASE_F2_4	PS51432	AP endonucleases family 2 profile.	END4_ECOLI	1-280	1	A:1-279 -
2	AP_NUCLEASE_F2_1	PS00729	AP endonucleases family 2 signature 1.	END4_ECOLI	69-77	1	A:69-77 -
3	AP_NUCLEASE_F2_2	PS00730	AP endonucleases family 2 signature 2.	END4_ECOLI	175-182	1	A:175-182 -
4	AP_NUCLEASE_F2_3	PS00731	AP endonucleases family 2 signature 3.	END4_ECOLI	215-231	1	A:215-231 -

Biological Unit 2 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AP_NUCLEASE_F2_4	PS51432	AP endonucleases family 2 profile.	END4_ECOLI	1-280	1	- B:1-279
2	AP_NUCLEASE_F2_1	PS00729	AP endonucleases family 2 signature 1.	END4_ECOLI	69-77	1	- B:69-77
3	AP_NUCLEASE_F2_2	PS00730	AP endonucleases family 2 signature 2.	END4_ECOLI	175-182	1	- B:175-182
4	AP_NUCLEASE_F2_3	PS00731	AP endonucleases family 2 signature 3.	END4_ECOLI	215-231	1	- B:215-231

(no "Exon" information available for 2NQJ)

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: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 d2nqja_ A: Endonuclease IV                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2nqjA00 A:1-279 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhh.hhh.eeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeee..ee.....hhhhhhhhhhhhhhhhhhh....eeeee.......ee..hhhhhhhhhhh..hhh.eeeeeehhhhhhhh....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
                 2nqj A   1 MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILQTINPDIWAEEIAWLKAQQ 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: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 d2nqjb_ B: Endonuclease IV                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2nqjB00 B:1-279 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ------------------AP_endonuc_2-2nqjB01 B:19-239                                                                                                                                                                                                ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------AP_endonuc_2-2nqjB02 B:19-239                                                                                                                                                                                                ---------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhh..hhh.eeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhh..hhh.eeeeeehhhhhhhh....hhhhhhhhhhhhhhhhhhh.eeeeee.ee..........ee.......hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AP_NUCLEASE_F2_4  PDB: B:1-279 UniProt: 1-280                                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------AP_NUCLEA-------------------------------------------------------------------------------------------------AP_NUCLE--------------------------------AP_NUCLEASE_F2_3 ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nqj B   1 MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILQTINPDIWAEEIAWLKAQQ 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 C from PDB  Type:DNA  Length:15
                                               
                 2nqj C 301 GCGTCCxCGACGACG 315
                                  |310     
                                307-3DR

Chain D from PDB  Type:DNA  Length:15
                                               
                 2nqj D 331 CGTCGTCGGGGACGC 345
                                   340

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Xylose isomerase-like (125)

Family: Endonuclease IV (8)

Protein domain: Endonuclease IV (6)

Escherichia coli [TaxId: 562] (5)

1a	d2nqja_	A:
1b	d2nqjb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Divalent-metal-dependent TIM barrel enzymes (98)

[unclassified] (4)

1a	2nqjA00	A:1-279
1b	2nqjB00	B:1-279

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Escherichia coli (strain K12) (5)

1a	AP_endonuc_2-2nqjB01	B:19-239
1b	AP_endonuc_2-2nqjB02	B:19-239

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	2nqj
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	END4_ECOLI \| P0A6C1	:	1qtw 1qum 2nq9 2nqh 4k1g

2nq9	HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV (ENDO IV) Y72A MUTANT BOUND TO DAMAGED DNA
2nqh	HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV (ENDO IV) E261Q MUTANT

Description

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