3T4H - JenaLib

Title :   CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(III) AND N-OXALYL-S-(3-NITROBENZYL)-L-CYSTEINE

Authors :   J. Ma, W. S. Aik, M. A. Mcdonough, C. J. Schofield

Date :   26 Jul 11 (Deposition) - 07 Mar 12 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : B

Keywords :   Double-Stranded Beta-Helix, Nucleic Acid Demethylase, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. C. Woon, M. Demetriades, E. A. Bagg, W. Aik, S. M. Krylova, J. H. Ma, M. Chan, L. J. Walport, D. W. Wegman, K. N. Dack, M. A. Mcdonough, S. N. Krylov, C. J. Schofield
Dynamic Combinatorial Mass Spectrometry Leads To Inhibitors Of A 2-Oxoglutarate-Dependent Nucleic Acid Demethylase.
J. Med. Chem. V. 55 2173 2012
PubMed-ID: 22263962 | Reference-DOI: 10.1021/JM201417E

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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 B from PDB  Type:PROTEIN  Length:201
 aligned with ALKB_ECOLI | P05050 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:201
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
           ALKB_ECOLI    14 PLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGK 214
               SCOP domains d3t4hb_ B: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee......hhhhhhhhhhhhhhhh...............eeeeee..eeeee..eeeee.............hhhhhhhhhhhhhhh........eeeeeee.....eeee...........eeeeeee..eeeee.........eeeee....eeee.hhhhhh.eee..............eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: B:113-213 UniProt: 113-213                                                           - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t4h B  14 PLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGK 214
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain 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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	3t4h
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	1.14.11.-
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

2fd8	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2- OXOGLUTARATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T
2fdf	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH CO(II), 2- OXOGLUTARATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T
2fdg	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), SUCCINATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T
2fdh	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II), 2- OXOGLUTARATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T
2fdi	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2- OXOGLUTARATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T (AIR 3 HOURS)
2fdj	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II) AND SUCCINATE
2fdk	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2- OXOGLUTARATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T (AIR 9 DAYS)
3bi3	X-RAY STRUCTURE OF ALKB PROTEIN BOUND TO DSDNA CONTAINING 1MEA/A WITH COFACTORS
3bie	X-RAY STRUCTURE OF E COLI ALKB BOUND TO DSDNA CONTAINING 1MEA/T WITH MN AND 2KG
3bkz	X-RAY STRUCTURE OF E COLI ALKB CROSSLINKED TO DSDNA IN THE ACTIVE SITE
3h8o	STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3-MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM
3h8r	STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3-MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM
3h8x	STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3-MEC IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM
3i2o	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2- OXOGLUTARATE AND METHYLATED TRINUCLEOTIDE T-MEA-T
3i3m	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II), 2- OXOGLUTARATE AND METHYLATED TRINUCLEOTIDE T-MEC-T
3i3q	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH MN(II) AND 2- OXOGLUTARATE
3i49	CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH FE(II), 2- OXOGLUTARATE AND METHYLATED TRINUCLEOTIDE T-MEC-T
3khb	CRYSTAL STRUCTURE OF ESCHERICHIA COLI ALKB WITH CO(II) AND 2-OG
3khc	CRYSTAL STRUCTURE OF ESCHERICHIA COLI ALKB IN COMPLEX WITH SSDNA CONTAINING A 1-METHYLGUANINE LESION
3o1m	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1o	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1p	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1r	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1s	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1t	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1u	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3o1v	IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR DIOXYGENASE
3t3y
3t4v

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