4B5G - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS (CRYSTAL FORM 2)

Authors :   D. Lu, J. Silhan, J. T. Macdonald, E. P. Carpenter, K. Jensen, C. M. Tang, G. S. Baldwin, P. S. Freemont

Date :   03 Aug 12 (Deposition) - 17 Oct 12 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A,B,C,U,V,W,X,Y,Z
Biol. Unit 1: A,U,V  (1x)
Biol. Unit 2: B,W,X  (1x)
Biol. Unit 3: C,Y,Z  (1x)

Keywords :   Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lu, J. Silhan, J. T. Macdonald, E. P. Carpenter, K. Jensen, C. M. Tang G. S. Baldwin, P. S. Freemont
Structural Basis For The Recognition And Cleavage Of Abasic Dna In Neisseria Meningitidis.
Proc. Natl. Acad. Sci. Usa V. 109 16852 2012
PubMed-ID: 23035246 | Reference-DOI: 10.1073/PNAS.1206563109

Molecule 1 - EXODEOXYRIBONUCLEASE
	Chains	:	A, B, C
	EC Number	:	3.1.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	487
	Synonym	:	NEISSERIA AP ENDONUCLEASE

*Molecule 2 - 5'-D(GPCPTPAPCP(3DR)PCPAPTPCPGP)-3'**
	Chains	:	U, W, Y
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	487
	Synonym	:	DNA 11MER CONTAINING ABASIC RESIDUE
	Synthetic	:	YES

*Molecule 3 - 5'-D(CPGPAPTPGPGPGPTPAPGPCP)-3'**
	Chains	:	V, X, Z
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	487
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9
Asymmetric Unit	:	A	B	C	U	V	W	X	Y	Z
Biological Unit 1 (1x)	:	A			U	V
Biological Unit 2 (1x)	:		B				W	X
Biological Unit 3 (1x)	:			C					Y	Z

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	3DR	3	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(no "Site" information available for 4B5G)

(no "SS Bond" information available for 4B5G)

(no "Cis Peptide Bond" information available for 4B5G)

(no "SAP(SNP)/Variant" information available for 4B5G)

(no "PROSITE Motif" information available for 4B5G)

(no "Exon" information available for 4B5G)

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: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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhh...eeeee..............hhhhheeeee.........eeeee.....eeee...hhhhhh...eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhh.............hhhhhhhhhhhhhh...eehhhhhh.......ee...........ee..eeeeehhhhhh.eeeeee...........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5g 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

Chain B 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhh...eeeee..............hhhhheeeee.........eeeee.....eeee...hhhhhh...eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhh.............hhhhhhhhhhhhh....eehhhhhh.......ee...........ee..eeeeehhhhhh.eeeeee...........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5g B   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

Chain C 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhh...eeeee..............hhhhheeeee.........eeeee.....eeee...hhhhhh...eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhh.............hhhhhhhhhhhhhh...eehhhhhh........................eeeeehhhhhh.eeeeee...........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b5g C   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

Chain U from PDB  Type:DNA  Length:11
                                           
                 4b5g U  31 GCTACxCATCG  41
                                 |  40 
                                36-3DR

Chain V from PDB  Type:DNA  Length:11
                                           
                 4b5g V  42 CGATGGGTAGC  52
                                    51

Chain W from PDB  Type:DNA  Length:11
                                           
                 4b5g W  31 GCTACxCATCG  41
                                 |  40 
                                36-3DR

Chain X from PDB  Type:DNA  Length:11
                                           
                 4b5g X  42 CGATGGGTAGC  52
                                    51

Chain Y from PDB  Type:DNA  Length:11
                                           
                 4b5g Y  31 GCTACxCATCG  41
                                 |  40 
                                36-3DR

Chain Z from PDB  Type:DNA  Length:11
                                           
                 4b5g Z  42 CGATGGGTAGC  52
                                    51

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 "SCOP Domain" information available for 4B5G)

(no "CATH Domain" information available for 4B5G)

(no "Pfam Domain" information available for 4B5G)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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.

Asymmetric Unit
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Biological Units
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	4b5g
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	3.1.11.2
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UniProtKB/TrEMBL
	Q7DD47_NEIMB \| Q7DD47	:	2jc5 4b5f 4b5h 4b5i 4b5j 4b5m

4b5f	SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS (CRYSTAL FORM 1)
4b5h	SUBSTATE BOUND INACTIVE MUTANT OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL IONS
4b5i	PRODUCT COMPLEX OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL IONS
4b5j	NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN ADENINE BASE
4b5m	NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH A CYTOSINE ORPHAN BASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (8, 16)

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