1PVS - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   3-METHYLADENINE GLCOSYLASE II(ALKA) HYPOXANTHINE COMPLEX

Authors :   M. Teale

Date :   28 Jun 03 (Deposition) - 08 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Alka, Hypoxanthine, Dna Glycosylase, Dna Repair, Reaction- Product Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Teale, J. Symersky, L. Delucas
3-Methyladenine-Dna Glycosylase Ii: The Crystal Structure Of An Alka-Hypoxanthine Complex Suggests The Possibility Of Product Inhibition.
Bioconjug. Chem. V. 13 403 2002
PubMed-ID: 12009927 | Reference-DOI: 10.1021/BC015527V
(for further references see the PDB file header)

Molecule 1 - DNA-3-METHYLADENINE GLYCOSYLASE II
	Chains	:	A, B
	EC Number	:	3.2.2.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ALKA OR AIDA OR B2068
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	3-METHYLADENINE-DNA GLYCOSYLASE II, INDUCIBLE, TAG II, DNA-3-METHYLADENINE GLYCOSIDASE II

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	7HP	2	Ligand/Ion	7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	7HP	1	Ligand/Ion	7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	7HP	1	Ligand/Ion	7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:123 , GLN B:124 , LEU B:125 , VAL B:126 , TRP B:218 , ASP B:237 , ASP B:238 , TYR B:239	BINDING SITE FOR RESIDUE 7HP B 700
2	AC2	SOFTWARE	GLY A:123 , GLN A:124 , LEU A:125 , VAL A:126 , TRP A:218 , ASP A:237 , ASP A:238 , TYR A:239 , HOH A:811 , HOH A:876	BINDING SITE FOR RESIDUE 7HP A 800

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

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 1PVS)

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 1PVS)

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 d1pvsa2 A:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d1pvsa1 A:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 1pvsA01 A:1-112 DNA-3-methyladenine glycosylase ii                                                              1pvsA02 A:113-230 Hypothetical protein; domain 2                                                                      1pvsA03 A:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhee.......ee..hhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pvs 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 d1pvsb2 B:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d1pvsb1 B:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 1pvsB01 B:1-112 DNA-3-methyladenine glycosylase ii                                                              1pvsB02 B:113-230 Hypothetical protein; domain 2                                                                      1pvsB03 B:231-282                                    CATH domains
           Pfam domains (1) AlkA_N-1pvsB03 B:1-112                                                                                          -----HhH-GPD-1pvsB01 B:118-263                                                                                                                         ------------------- Pfam domains (1)
           Pfam domains (2) AlkA_N-1pvsB04 B:1-112                                                                                          -----HhH-GPD-1pvsB02 B:118-263                                                                                                                         ------------------- Pfam domains (2)
         Sec.struct. author .eeee.....hhhhhhhhhhhhh....eee....eeeeeee..eeeeeeeeeehhh.eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.............hhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pvs 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

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HHH (112)

Family: HhH-GPD (47)

Escherichia coli (strain K12) (15)

1a	HhH-GPD-1pvsB01	B:118-263
1b	HhH-GPD-1pvsB02	B:118-263

Clan: TBP-like (48)

Family: AlkA_N (5)

Escherichia coli (strain K12) (5)

2a	AlkA_N-1pvsB03	B:1-112
2b	AlkA_N-1pvsB04	B:1-112

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.

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(no "Related Entries Specified in the PDB File" available for 1PVS)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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