1DIZ | PD0099 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

Authors :   T. Hollis, Y. Ichikawa, T. E. Ellenberger

Date :   30 Nov 99 (Deposition) - 20 Mar 00 (Release) - 27 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   3-Methyladenine Dna Glycosylase, Alka, Helix-Hairpin-Helix, Protein- Dna Complex, 1-Azaribose, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hollis, Y. Ichikawa, T. Ellenberger
Dna Bending And A Flip-Out Mechanism For Base Excision By The Helix-Hairpin-Helix Dna Glycosylase, Escherichia Coli Alka.
Embo J. V. 19 758 2000
PubMed-ID: 10675345 | Reference-DOI: 10.1093/EMBOJ/19.4.758

*Molecule 1 - DNA (5'-D(GPAPCPAPTPGPAP(NRI)PTPGPCPCPT)-3')**
	Chains	:	C, E
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN E. COLI
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(GPGPCPAPAPTPCPAPTPGPTPCPA)-3')**
	Chains	:	D, F
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN E. COLI
	Synthetic	:	YES

Molecule 3 - 3-METHYLADENINE DNA GLYCOSYLASE II
	Chains	:	A, B
	EC Number	:	3.2.2.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	3-METHYLADENINE-DNA GLYCOSYLASE II, INDUCIBLE, TAG II, ALKA

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A				E	F
Biological Unit 2 (1x)	:		B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION
2	NRI	2	Mod. Nucleotide	PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)ESTER

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NRI	1	Mod. Nucleotide	PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)ESTER

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NRI	1	Mod. Nucleotide	PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)ESTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:210 , PHE B:212 , ILE B:215 , HOH B:844 , DC C:11	BINDING SITE FOR RESIDUE NA B 824
2	AC2	SOFTWARE	GLN A:210 , PHE A:212 , ILE A:215 , HOH A:850 , DC E:11	BINDING SITE FOR RESIDUE NA A 825

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

Asymmetric Unit

No.	Residues
1	Pro A:8	-	Pro A:9
2	Lys A:261	-	Pro A:262
3	Pro B:8	-	Pro B:9
4	Lys B:261	-	Pro B:262

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALKYLBASE_DNA_GLYCOS	PS00516	Alkylbase DNA glycosidases alkA family signature.	3MG2_ECOLI	214-238	2	A:214-238 B:214-238

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALKYLBASE_DNA_GLYCOS	PS00516	Alkylbase DNA glycosidases alkA family signature.	3MG2_ECOLI	214-238	1	A:214-238 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALKYLBASE_DNA_GLYCOS	PS00516	Alkylbase DNA glycosidases alkA family signature.	3MG2_ECOLI	214-238	1	- B:214-238

(no "Exon" information available for 1DIZ)

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:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    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       280  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d1diza2 A:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d1diza1 A:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 1dizA01 A:1-112 DNA-3-methyladenine glycosylase ii                                                              1dizA02 A:113-230 Hypothetical protein; domain 2                                                                      1dizA03 A:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhh.....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1diz A   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    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       280

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    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       280  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d1dizb2 B:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d1dizb1 B:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 1dizB01 B:1-112 DNA-3-methyladenine glycosylase ii                                                              1dizB02 B:113-230 Hypothetical protein; domain 2                                                                      1dizB03 B:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.ee..eeeee...hhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....hhhhhhhhhhhhh...........hhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1diz B   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    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       280

Chain C from PDB  Type:DNA  Length:13
                                             
                 1diz C   1 GACATGAxTGCCT  13
                                   |10   
                                   8-NRI

Chain D from PDB  Type:DNA  Length:13
                                             
                 1diz D  14 GGCAATCATGTCA  26
                                    23

Chain E from PDB  Type:DNA  Length:13
                                             
                 1diz E   1 GACATGAxTGCCT  13
                                   |10   
                                   8-NRI

Chain F from PDB  Type:DNA  Length:13
                                             
                 1diz F  14 GGCAATCATGTCA  26
                                    23

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: TATA-Binding Protein (118)

Homologous Superfamily: DNA-3-methyladenine glycosylase ii (11)

[unclassified] (1)

1a	1dizA01	A:1-112
1b	1dizB01	B:1-112

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Endonuclease Iii, domain 2 (65)

Homologous Superfamily: Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) (65)

[unclassified] (30)

2a	1dizA03	A:231-282
2b	1dizB03	B:231-282

Topology: Endonuclease III; domain 1 (74)

Homologous Superfamily: Hypothetical protein; domain 2 (73)

[unclassified] (31)

3a	1dizA02	A:113-230
3b	1dizB02	B:113-230

(no "Pfam Domain" information available for 1DIZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (3MG2_ECOLI | P04395)

molecular function
	GO:0008725	DNA-3-methyladenine glycosylase activity	Catalysis of the reaction: DNA containing 3-methyladenine + H2O = DNA with abasic site + 3-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methyladenine and the deoxyribose sugar to remove the 3-methyladenine, leaving an abasic site.
	GO:0052822	DNA-3-methylguanine glycosylase activity	Catalysis of the reaction: DNA containing 3-methylguanine + H2O = DNA with abasic site + 3-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methylguanine and the deoxyribose sugar to remove the 3-methylguanine, leaving an abasic site.
	GO:0052821	DNA-7-methyladenine glycosylase activity	Catalysis of the reaction: DNA containing 7-methyladenine + H2O = DNA with abasic site + 7-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methyladenine and the deoxyribose sugar to remove the 7-methyladenine, leaving an abasic site.
	GO:0043916	DNA-7-methylguanine glycosylase activity	Catalysis of the reaction: DNA containing 7-methylguanine + H2O = DNA with abasic site + 7-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methylguanine and the deoxyribose sugar to remove the 7-methylguanine, leaving an abasic site.
	GO:0003905	alkylbase DNA N-glycosylase activity	Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site.
	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: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.
biological process
	GO:0006307	DNA dealkylation involved in DNA repair	The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:261 - Pro A:262	[ RasMol ]
		Lys B:261 - Pro B:262	[ RasMol ]
		Pro A:8 - Pro A:9	[ RasMol ]
		Pro B:8 - Pro B:9	[ RasMol ]

Biological Units
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	3MG2_ECOLI \| P04395	:	1mpg 1pvs 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu 3d4v 3ogd 3oh6 3oh9

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Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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