3UBT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF C71S MUTANT OF DNA CYTOSINE-5 METHYLTRANSFERASE M.HAEIII BOUND TO DNA

Authors :   G. L. Verdine, A. Didovyk

Date :   24 Oct 11 (Deposition) - 03 Oct 12 (Release) - 19 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,Y
Biol. Unit 1: G,H,Y  (1x)
Biol. Unit 2: A,E,F  (1x)
Biol. Unit 3: B,C,D  (1x)

Keywords :   Protein-Dna Complex, Dna Cytosine-5 Methyltransferase, Dna Binding, S-Adenosyl Methionine Binding, Cytosine-5 Dna Methylation, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Didovyk, G. L. Verdine
Structural Origins Of Dna Target Selection And Nucleobase Extrusion By A Dna Cytosine Methyltransferase.
J. Biol. Chem. V. 287 40099 2012
PubMed-ID: 23012373 | Reference-DOI: 10.1074/JBC.M112.413054

Molecule 1 - MODIFICATION METHYLASE HAEIII
	Chains	:	Y, A, B
	EC Number	:	2.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHN1
	Expression System Strain	:	LC1061
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HAEIIIM
	Mutation	:	YES
	Organism Common	:	KOCH-WEEKS BACILLUS
	Organism Scientific	:	HAEMOPHILUS AEGYPTIUS
	Organism Taxid	:	197575
	Synonym	:	M.HAEIII, CYTOSINE-SPECIFIC METHYLTRANSFERASE HAEIII

*Molecule 2 - 5'-D(TPGPGPCPCPA)-3'*
	Chains	:	D, E, F, G, H, C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9
Asymmetric Unit	:	A	B	C	D	E	F	G	H	Y
Biological Unit 1 (1x)	:							G	H	Y
Biological Unit 2 (1x)	:	A				E	F
Biological Unit 3 (1x)	:		B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	2PE	3	Ligand/Ion	NONAETHYLENE GLYCOL
2	ATP	3	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	3	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DC H:11 , SER Y:241	BINDING SITE FOR RESIDUE CL Y 332
2	AC2	SOFTWARE	SER A:258 , LYS A:259 , GLU Y:29 , TYR Y:30 , ASP Y:50 , ILE Y:51 , LEU Y:90 , HOH Y:359 , HOH Y:368 , HOH Y:461 , HOH Y:491 , HOH Y:501	BINDING SITE FOR RESIDUE ATP Y 333
3	AC3	SOFTWARE	GLU B:29 , TYR B:30 , ASP B:50 , ILE B:51 , PRO B:70 , LEU B:90 , LYS B:302 , SER Y:258 , LYS Y:259 , ASN Y:260 , HOH Y:344 , HOH Y:424 , HOH Y:463	BINDING SITE FOR RESIDUE ATP Y 334
4	AC4	SOFTWARE	PRO B:192 , GLN B:250 , LYS Y:182 , TRP Y:186 , TRP Y:231 , ASN Y:232	BINDING SITE FOR RESIDUE 2PE Y 335
5	AC5	SOFTWARE	SER A:241 , DC F:11	BINDING SITE FOR RESIDUE CL A 332
6	AC6	SOFTWARE	GLU A:29 , TYR A:30 , ASP A:50 , ILE A:51 , ASN A:306 , HOH A:361 , HOH A:457 , HOH A:524 , HOH A:565 , LYS B:259	BINDING SITE FOR RESIDUE ATP A 333
7	AC7	SOFTWARE	LYS A:182 , TRP A:186 , PRO Y:192 , PRO Y:194	BINDING SITE FOR RESIDUE 2PE A 334
8	AC8	SOFTWARE	SER B:241 , DC C:11 , HOH Y:479	BINDING SITE FOR RESIDUE CL B 332
9	AC9	SOFTWARE	PRO A:194 , ALA A:195 , LYS B:182 , TRP B:186 , TRP B:231	BINDING SITE FOR RESIDUE 2PE B 333

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

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

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

Asymmetric Unit (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH3_HAEAE	1-327	3	A:1-327 B:1-327 Y:1-327
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH3_HAEAE	63-75	3	A:63-75 B:63-75 Y:63-75
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH3_HAEAE	302-320	3	A:302-320 B:302-320 Y:302-320

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH3_HAEAE	1-327	1	- - Y:1-327
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH3_HAEAE	63-75	1	- - Y:63-75
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH3_HAEAE	302-320	1	- - Y:302-320

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH3_HAEAE	1-327	1	A:1-327 - -
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH3_HAEAE	63-75	1	A:63-75 - -
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH3_HAEAE	302-320	1	A:302-320 - -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH3_HAEAE	1-327	1	- B:1-327 -
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH3_HAEAE	63-75	1	- B:63-75 -
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH3_HAEAE	302-320	1	- B:302-320 -

(no "Exon" information available for 3UBT)

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:328
 aligned with MTH3_HAEAE | P20589 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:328
                                    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       290       300       310       320        
           MTH3_HAEAE     1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICK 328
               SCOP domains d3ubta_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhh..eeeeeee....hhhhhhhhh..eeee......hhhhh....eee...hhhh.ee..ee....hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh..hhhhhhhhhhhhhhheeeeeeeee.hhh......eeeeeeeee.hhh..............hhhhhhhhh...ee.hhhhh.hhhhh.....ee.....hhhhhh..............................eeee..eee....hhhhh...hhhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SAM_MT_C5  PDB: A:1-327 UniProt: 1-327                                                                                                                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         -------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubt A   1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPSQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICK 328
                                    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       290       300       310       320

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with MTH3_HAEAE | P20589 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:328
                                    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       290       300       310       320        
           MTH3_HAEAE     1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICK 328
               SCOP domains d3ubtb_ B: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhh..eeeeee.....hhhhhhhhh..eee.......hhhhh....eee...hhhhh..........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh..hhhhhhhhhhhhhhheeeeeeeee.hhh......eeeeeeeee.hhh.............hhhhhhhhhh...ee.......hhhhh.....ee.....hhhhhh..............................eeee..eee....hhhhh...hhhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SAM_MT_C5  PDB: B:1-327 UniProt: 1-327                                                                                                                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         -------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubt B   1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPSQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICK 328
                                    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       290       300       310       320

Chain C from PDB  Type:DNA  Length:6
                                      
                 3ubt C   7 TGGCCA  12

Chain D from PDB  Type:DNA  Length:6
                                      
                 3ubt D   4 TGGCCA   9

Chain E from PDB  Type:DNA  Length:6
                                      
                 3ubt E   4 TGGCCA   9

Chain F from PDB  Type:DNA  Length:6
                                      
                 3ubt F   7 TGGCCA  12

Chain G from PDB  Type:DNA  Length:6
                                      
                 3ubt G   4 TGGCCA   9

Chain H from PDB  Type:DNA  Length:6
                                      
                 3ubt H   7 TGGCCA  12

Chain Y from PDB  Type:PROTEIN  Length:328
 aligned with MTH3_HAEAE | P20589 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:328
                                    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       290       300       310       320        
           MTH3_HAEAE     1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICK 328
               SCOP domains d3ubty_ Y: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhh..eeeeeee....hhhhhhhhh..eeee.hhhhhhhhhh....eee...hhhh.ee..ee....hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh..hhhhhhhhhhhhhhheeeeeeeee.hhh......eeeeeeeee.hhh.............hhhhhhhhhh...ee.hhhhh.hhhhh.....ee.......hhhhh.............................eeee..eee....hhhhh...hhhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SAM_MT_C5  PDB: Y:1-327 UniProt: 1-327                                                                                                                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         -------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubt Y   1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPSQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSALEICK 328
                                    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       290       300       310       320

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 "CATH Domain" information available for 3UBT)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,Y (MTH3_HAEAE | P20589)

molecular function
	GO:0003886	DNA (cytosine-5-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
	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:0090116	C-5 methylation of cytosine	The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule.
	GO:0009307	DNA restriction-modification system	A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

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	Cis Peptide Bonds
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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