3I3Q - JenaLib

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Title :   CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II) AND 2-OXOGLUTARATE

Authors :   B. Yu, J. F. Hunt

Date :   30 Jun 09 (Deposition) - 25 Aug 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Beta Jellyroll, Dioxygenase, Dna Damage, Dna Repair, Iron, Metal- Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Yu, J. F. Hunt
Enzymological And Structural Studies Of The Mechanism Of Promiscuous Substrate Recognition By The Oxidative Dna Repair Enzyme Alkb.
Proc. Natl. Acad. Sci. Usa V. 106 14315 2009
PubMed-ID: 19706517 | Reference-DOI: 10.1073/PNAS.0812938106

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 12-216
	Gene	:	AIDD, ALKB, B2212, JW2200
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	ALKYLATED DNA REPAIR PROTEIN ALKB

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:118 , ASN A:120 , TYR A:122 , LEU A:128 , HIS A:131 , ASP A:133 , HIS A:187 , ILE A:189 , ARG A:204 , ASN A:206 , THR A:208 , ARG A:210 , MN A:301 , HOH A:606 , HOH A:611 , HOH A:619 , HOH A:826	BINDING SITE FOR RESIDUE AKG A 401
2	AC2	SOFTWARE	HIS A:131 , ASP A:133 , HIS A:187 , AKG A:401 , HOH A:611	BINDING SITE FOR RESIDUE MN A 301
3	AC3	SOFTWARE	LEU B:118 , ASN B:120 , TYR B:122 , LEU B:128 , HIS B:131 , ASP B:133 , HIS B:187 , ILE B:189 , ARG B:204 , ASN B:206 , THR B:208 , ARG B:210 , MN B:302 , HOH B:618 , HOH B:621 , HOH B:743 , HOH B:938	BINDING SITE FOR RESIDUE AKG B 402
4	AC4	SOFTWARE	HIS B:131 , ASP B:133 , HIS B:187 , AKG B:402 , HOH B:743	BINDING SITE FOR RESIDUE MN B 302

(no "SS Bond" information available for 3I3Q)

(no "Cis Peptide Bond" information available for 3I3Q)

(no "SAP(SNP)/Variant" information available for 3I3Q)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE2OG_OXY	PS51471	Fe(2+) 2-oxoglutarate dioxygenase domain profile.	ALKB_ECOLI	113-213	2	A:113-213 B:113-213

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE2OG_OXY	PS51471	Fe(2+) 2-oxoglutarate dioxygenase domain profile.	ALKB_ECOLI	113-213	1	A:113-213 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE2OG_OXY	PS51471	Fe(2+) 2-oxoglutarate dioxygenase domain profile.	ALKB_ECOLI	113-213	1	- B:113-213

(no "Exon" information available for 3I3Q)

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:203
 aligned with ALKB_ECOLI | P05050 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:203
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
           ALKB_ECOLI    13 EPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKK 215
               SCOP domains d3i3qa_ A: automated matches                                                                                                                                                                                SCOP domains
               CATH domains 3i3qA00 A:13-215 Clavaminate synthase-like domains                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee......hhhhhhhhhhhhhhhh...............eeeee...eeeee..eeeee.............hhhhhhhhhhhhhhh........eeeeeee.....eeee...........eeeeeee..eeeee.........eeeee....eeeehhhhh...eee..............eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:113-213 UniProt: 113-213                                                           -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3q A  13 EPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKK 215
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with ALKB_ECOLI | P05050 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:203
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
           ALKB_ECOLI    12 QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGK 214
               SCOP domains d3i3qb_ B: automated matches                                                                                                                                                                                SCOP domains
               CATH domains 3i3qB00 B:12-214 Clavaminate synthase-like domains                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee......hhhhhhhhhhhhhhhh...............eeeee...eeeee..eeeee.............hhhhhhhhhhhhhhh........eeeeeee.....eeee...........eeeeeee..eeeee.........eeeee....eeeehhhhh...eee..............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: B:113-213 UniProt: 113-213                                                           - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i3q B  12 QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGK 214
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: AlkB-like (29)

Protein domain: automated matches (18)

Escherichia coli K-12 [TaxId: 83333] (18)

1a	d3i3qa_	A:
1b	d3i3qb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Clavaminate synthase-like domains (16)

Escherichia coli. Organism_taxid: 83333. Strain: k-12. (4)

1a	3i3qA00	A:13-215
1b	3i3qB00	B:12-214

(no "Pfam Domain" information available for 3I3Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ALKB_ECOLI | P05050)

molecular function
	GO:0043734	DNA-N1-methyladenine dioxygenase activity	Catalysis of the oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde.
	GO:0051747	cytosine C-5 DNA demethylase activity	Catalysis of the reaction: methyl-dCpdG DNA + H2O = dCpdG DNA + methanol. This reaction is the hydrolytic removal of the methyl group on the 5 position of cytosine in DNA.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035515	oxidative RNA demethylase activity	Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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:0080111	DNA demethylation	The removal of a methyl group from one or more nucleotides within an DNA molecule.
	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:0042245	RNA repair	Any process that results in the repair of damaged RNA.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0070989	oxidative demethylation	The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
	GO:0035552	oxidative single-stranded DNA demethylation	Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
	GO:0035553	oxidative single-stranded RNA demethylation	Removal of the methyl group from one or more nucleotides within a single-stranded RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.

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3i49

Description

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Ligands, Modified Residues, Ions (2, 4)

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