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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS O6-METHYLGUANINE METHYLTRANSFERASE

Authors :   R. Miggiano, V. Casazza, S. Garavaglia, M. Ciaramella, G. Perugino, M. F. Rossi

Date :   02 Apr 13 (Deposition) - 17 Apr 13 (Release) - 12 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Miggiano, V. Casazza, S. Garavaglia, M. Ciaramella, G. Perugino, M. Rizzi, F. Rossi
Biochemical And Structural Studies Of The Mycobacterium Tuberculosis O6-Methylguanine Methyltransferase And Mutated Variants.
J. Bacteriol. V. 195 2728 2013
PubMed-ID: 23564173 | Reference-DOI: 10.1128/JB.02298-12

Molecule 1 - METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.1.63
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET16B
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	6-O-METHYLGUANINE-DNA METHYLTRANSFERASE, MGMT, O-6-METHYLGUANINE-DNA-ALKYLTRANSFERASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:28 , ARG A:145 , HOH A:2011 , HOH A:2107	BINDING SITE FOR RESIDUE GOL A1166
2	AC2	SOFTWARE	HIS A:39 , PHE A:65 , VAL A:67 , LEU A:69 , LEU A:85 , ILE A:123 , HOH A:2047	BINDING SITE FOR RESIDUE GOL A1167

(no "SS Bond" information available for 4BHB)

(no "Cis Peptide Bond" information available for 4BHB)

(no "SAP(SNP)/Variant" information available for 4BHB)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MGMT	PS00374	Methylated-DNA--protein-cysteine methyltransferase active site.	OGT_MYCTO	124-130	1	A:124-130
1	MGMT	PS00374		OGT_MYCTU	124-130	1	A:124-130

(no "Exon" information available for 4BHB)

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:165
 aligned with OGT_MYCTO | P9WJW4 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            OGT_MYCTO     1 MIHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeeee..eeeeee......hhhhhhhee....hhhhhhhhhhhhh..............hhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhh.......hhhh............hhhhhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------MGMT   ----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhb A   1 MVHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain A from PDB  Type:PROTEIN  Length:165
 aligned with OGT_MYCTU | P9WJW5 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            OGT_MYCTU     1 MIHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeeee..eeeeee......hhhhhhhee....hhhhhhhhhhhhh..............hhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhh.......hhhh............hhhhhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------MGMT   ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bhb A   1 MVHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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 '\|'

(no "SCOP Domain" information available for 4BHB)

(no "CATH Domain" information available for 4BHB)

(no "Pfam Domain" information available for 4BHB)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OGT_MYCTO | P9WJW4)

molecular function
	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:0003908	methylated-DNA-[protein]-cysteine S-methyltransferase activity	Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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: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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (OGT_MYCTU | P9WJW5)

molecular function
	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:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0003908	methylated-DNA-[protein]-cysteine S-methyltransferase activity	Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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: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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0051409	response to nitrosative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	2.1.1.63
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UniProtKB/Swiss-Prot
	OGT_MYCTO \| P9WJW4	:	4bhc
	OGT_MYCTU \| P9WJW5	:	4bhc 4wx9 4wxc 4wxd

4bhc	CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS O6- METHYLGUANINE METHYLTRANSFERASE R37L VARIANT

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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