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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI ALKB IN COMPLEX WITH SSDNA CONTAINING A 1-METHYLGUANINE LESION

Authors :   T. Hollis, P. J. Holland

Date :   30 Oct 09 (Deposition) - 12 Jan 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Oxidoreductase, 1-Methylguanine, Alkb, 2-Oxoglutarate, Dioxygenase, Dna Damage, Dna Repair, Iron, Metal-Binding, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Holland, T. Hollis
Structural And Mutational Analysis Of Escherichia Coli Alkb Provides Insight Into Substrate Specificity And Dna Damage Searching.
Plos One V. 5 E8680 2010
PubMed-ID: 20084272 | Reference-DOI: 10.1371/JOURNAL.PONE.0008680

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-19B
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AIDD, ALKB, B2212, JW2200
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	ALKYLATED DNA REPAIR PROTEIN ALKB

*Molecule 2 - DNA (5'-D(PTPAP(MG1)PTPGPCPCPT)-3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(PGPCPAPT)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	CO	2	Ligand/Ion	COBALT (II) ION
3	MG1	1	Mod. Nucleotide	2'-DEOXY-1-METHYLGUANOSINE 5'-(DIHYDROGEN PHOSPHATE)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:131 , ASP A:133 , HIS A:187 , HOH A:245 , AKG A:400	BINDING SITE FOR RESIDUE CO A 217
2	AC2	SOFTWARE	LEU A:118 , ASN A:120 , TYR A:122 , LEU A:128 , HIS A:131 , ASP A:133 , SER A:145 , HIS A:187 , ILE A:189 , ARG A:204 , ASN A:206 , THR A:208 , CO A:217 , HOH A:220 , HOH A:230 , HOH A:245	BINDING SITE FOR RESIDUE AKG A 400
3	AC3	SOFTWARE	HIS B:131 , ASP B:133 , HIS B:187 , HOH B:260 , AKG B:401	BINDING SITE FOR RESIDUE CO B 217
4	AC4	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 , CO B:217 , HOH B:260 , HOH B:298 , MG1 C:4	BINDING SITE FOR RESIDUE AKG B 401

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

Asymmetric/Biological Unit

No.	Residues
1	Gly B:157	-	Gly B:158

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

Asymmetric/Biological 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

(no "Exon" information available for 3KHC)

Asymmetric/Biological 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:207
 aligned with ALKB_ECOLI | P05050 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:207
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       
           ALKB_ECOLI    10 PWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKE 216
               SCOP domains d3khca_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3khcA00 A:10-216 Clavaminate synthase-like domains                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeee.....hhhhhhhhhhhhhh.................eeeee...eee......eee.............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
                 3khc A  10 PWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKAEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKE 216
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with ALKB_ECOLI | P05050 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:207
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
           ALKB_ECOLI     9 EPWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKK 215
               SCOP domains d3khcb_ B: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3khcB00 B:9-215 Clavaminate synthase-like domains                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeee.....hhhhhhhhhhhhhhhh...............eeeee...eee......eee.............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
                 3khc B   9 EPWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKAEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKK 215
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain C from PDB  Type:DNA  Length:8
                                        
                 3khc C   2 TAgTGCCT   9
                              |     
                              4-MG1

Chain D from PDB  Type:DNA  Length:4
                                    
                 3khc D   4 GCAT   7

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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	d3khca_	A:
1b	d3khcb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Clavaminate synthase-like domains (16)

Escherichia coli k-12. Organism_taxid: 83333. Strain: k12. (2)

1a	3khcA00	A:10-216
1b	3khcB00	B:9-215

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

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly B:157 - Gly B:158	[ RasMol ]

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	3khc
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	1.14.11.-
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (16, 16)

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