1DCT | PDEB19 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA

Authors :   K. M. Reinisch, L. Chen, G. L. Verdine, W. N. Lipscomb

Date :   17 May 95 (Deposition) - 15 Sep 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,F,G,M,N
Biol. Unit 1: A,F,M  (1x)
Biol. Unit 2: B,G,N  (1x)

Keywords :   Enzyme, Cytosine Methylase, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Reinisch, L. Chen, G. L. Verdine, W. N. Lipscomb
The Crystal Structure Of Haeiii Methyltransferase Convalently Complexed To Dna: An Extrahelical Cytosine And Rearranged Base Pairing.
Cell(Cambridge, Mass. ) V. 82 143 1995
PubMed-ID: 7606780 | Reference-DOI: 10.1016/0092-8674(95)90060-8
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(APCPCPAPGPCPAPGPGP(C49) PCPAPCPCPAPGPTPG)-3')*
	Chains	:	F, G
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(TPCPAPCPTPGPGPTPGPGP(C5M) PCPTPGPCPTPGPG)-3')*
	Chains	:	M, N
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - PROTEIN (MODIFICATION METHYLASE HAEIII)
	Chains	:	A, B
	EC Number	:	2.1.1.73
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE BIOTYPE AEGYPTIUS
	Organism Taxid	:	725
	Strain	:	BIOTYPE AEGYPTIUS
	Synonym	:	CYTOSINE-SPECIFIC METHYLTRANSFERASE, HAEIII, M.HAEIII

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	F	G	M	N
Biological Unit 1 (1x)	:	A		F		M
Biological Unit 2 (1x)	:		B		G		N

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	5CM	2	Mod. Nucleotide	5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2	C49	2	Mod. Nucleotide	4-THIO,5-FLUORO,5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	5CM	1	Mod. Nucleotide	5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2	C49	1	Mod. Nucleotide	4-THIO,5-FLUORO,5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	5CM	1	Mod. Nucleotide	5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2	C49	1	Mod. Nucleotide	4-THIO,5-FLUORO,5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:166 , GLU B:233	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	ASN B:166 , DG M:17	BINDING SITE FOR RESIDUE CA B 1002
3	DAA	UNKNOWN	DG F:8 , DG F:9 , C49 F:10 , DC F:11 , DC M:12 , 5CM M:11 , DG M:10 , DG M:9	NULL
4	DAB	UNKNOWN	DG G:8 , DG G:9 , C49 G:10 , DC G:11 , DC N:12 , 5CM N:11 , DG N:10 , DG N:9	NULL

Asymmetric Unit

No.	Residues
1	B:245	-	B:280

(no "Cis Peptide Bond" information available for 1DCT)

(no "SAP(SNP)/Variant" information available for 1DCT)

Asymmetric Unit (3, 6)

	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	2	A:1-324 B:1-324
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH3_HAEAE	63-75	2	A:63-75 B:63-75
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH3_HAEAE	302-320	2	A:302-320 B: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	A:1-324 -
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 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	- B:1-324
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 1DCT)

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:324
 aligned with MTH3_HAEAE | P20589 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:324
                                    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 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSAL 324
               SCOP domains d1dcta_ A: DNA methylase HaeIII                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dctA01 A:1-142,A:155-172,A:312-324 Vaccinia Virus protein VP39                                                                               1dctA02     1dctA01           1dctA02 A:143-154,A:173-311 DNA Methylase, subunit A, domain 2                                                                             1dctA01       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhh..eeeeeee..hhhhhhhhhh...eeee.......hhh.....eeee..................hhhhhhhhhhhhhhhh...eeeeeeehhhh.hhhhhhhhhhhhhhhhhheeeeeeeeehhhh......eeeeeeeeehhh...............hhh..hhhhhh...........hhh..............hhhh..................hhh........................hhh.....hhhhhhhh............hhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) SAM_MT_C5  PDB: A:1-324 UniProt: 1-327                                                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) --------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         ---- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dct A   1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSAL 324
                                    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:324
 aligned with MTH3_HAEAE | P20589 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:324
                                    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 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSAL 324
               SCOP domains d1dctb_ B: DNA methylase HaeIII                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dctB01 B:1-142,B:155-172,B:312-324 Vaccinia Virus protein VP39                                                                               1dctB02     1dctB01           1dctB02 B:143-154,B:173-311 DNA Methylase, subunit A, domain 2                                                                             1dctB01       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhh...eeeeeee..hhhhhhhhhh...eeee..hhh..hhh.....eeee..................hhhhhhhhhhhhhhhh...eeeeeeehhhh.hhhhhhhhhhhhhhhh..eeeeeeeeehhh.......eeeeeeeeehhh...............hhh..hhh..............hhh..............hhhh..................hhh..........eeee..eee.....hhh.....hhhhhh..............hhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) SAM_MT_C5  PDB: B:1-324 UniProt: 1-327                                                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) --------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         ---- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dct B   1 MNLISLFSGAGGLDLGFQKAGFRIICANEYDKSIWKTYESNHSAKLIKGDISKISSDEFPKCDGIIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKKPIFFLAENVKGMMAQRHNKAVQEFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFRKELNINYLPPIPHLIKPTFKDVIWDLKDNPIPALDKNKTNGNKCIYPNHEYFIGSYSTIFMSRNRVRQWNEPAFTVQASGRQCQLHPQAPVMLKVSKNLNKFVEGKEHLYRRLTVRECARVQGFPDDFIFHYESLNDGYKMIGNAVPVNLAYEIAKTIKSAL 324
                                    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 F from PDB  Type:DNA  Length:18
                                                  
                 1dct F   1 ACCAGCAGGcCACCAGTG  18
                                    10        
                                    10-C49

Chain G from PDB  Type:DNA  Length:16
                                                
                 1dct G   3 CAGCAGGcCACCAGTG  18
                                   |12      
                                  10-C49

Chain M from PDB  Type:DNA  Length:18
                                                  
                 1dct M   1 TCACTGGTGGcCTGCTGG  18
                                    10|       
                                     11-5CM

Chain N from PDB  Type:DNA  Length:17
                                                 
                 1dct N   1 TCACTGGTGGcCTGCTG  17
                                    10|      
                                     11-5CM

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

[unclassified] (23)

1a	1dctA01	A:1-142,A:155-172,A:312-324
1b	1dctB01	B:1-142,B:155-172,B:312-324

Architecture: Alpha-Beta Complex (3881)

Topology: DNA Methylase; Chain A, domain 2 (31)

Homologous Superfamily: DNA Methylase, subunit A, domain 2 (31)

[unclassified] (15)

2a	1dctA02	A:143-154,A:173-311
2b	1dctB02	B:143-154,B:173-311

(no "Pfam Domain" information available for 1DCT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dct)

Biological Units
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(no "Related Entries Specified in the PDB File" available for 1DCT)

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (1, 1)

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