1G55 - JenaLib

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Title :   STRUCTURE OF HUMAN DNMT2, AN ENIGMATIC DNA METHYLTRANSFERASE HOMOLOGUE

Authors :   A. Dong, J. A. Yoder, X. Zhang, L. Zhou, T. H. Bestor, X. Cheng

Date :   30 Oct 00 (Deposition) - 17 Jan 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Human Dna Methyltransferase Homologue, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dong, J. A. Yoder, X. Zhang, L. Zhou, T. H. Bestor, X. Cheng
Structure Of Human Dnmt2, An Enigmatic Dna Methyltransferas Homolog That Displays Denaturant-Resistant Binding To Dna.
Nucleic Acids Res. V. 29 439 2001
PubMed-ID: 11139614 | Reference-DOI: 10.1093/NAR/29.2.439

Molecule 1 - DNA CYTOSINE METHYLTRANSFERASE DNMT2
	Chains	:	A
	EC Number	:	2.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:61 , LEU A:62 , HIS A:101 , ILE A:105 , ARG A:108 , LYS A:334 , HOH A:488	BINDING SITE FOR RESIDUE SO4 A 399
2	AC2	SOFTWARE	TYR A:10 , SER A:11 , GLY A:12 , VAL A:13 , GLY A:15 , ASP A:34 , VAL A:35 , ASN A:36 , LYS A:55 , THR A:56 , ILE A:57 , GLU A:58 , SER A:76 , PRO A:78 , SER A:98 , ASN A:375 , SER A:376 , HOH A:414 , HOH A:427 , HOH A:459 , HOH A:495 , HOH A:657	BINDING SITE FOR RESIDUE SAH A 392
3	AC3	SOFTWARE	HIS A:18 , ARG A:21 , GLU A:22 , CYS A:24 , ASN A:46 , PHE A:47 , GLU A:357 , HOH A:637	BINDING SITE FOR RESIDUE BME A 395
4	AC4	SOFTWARE	LEU A:279 , ASP A:281 , VAL A:291 , ILE A:301 , GLU A:302 , GLY A:303 , THR A:304 , GLY A:305	BINDING SITE FOR RESIDUE GOL A 397

(no "SS Bond" information available for 1G55)

(no "Cis Peptide Bond" information available for 1G55)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051961	H	101	Y	TRDMT_HUMAN	Polymorphism	11254413	A	H	101	Y

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	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.	TRDMT_HUMAN	4-391	1	A:4-391
2	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	TRDMT_HUMAN	371-389	1	A:371-389

Asymmetric/Biological Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000377799	1d	ENSE00002177384	chr10:17243681-17243570	112	TRDMT_HUMAN	1-22	22	1	A:2-22	21
1.4b	ENST00000377799	4b	ENSE00001771809	chr10:17216659-17216550	110	TRDMT_HUMAN	22-58	37	1	A:22-58	37
1.9	ENST00000377799	9	ENSE00000692747	chr10:17210916-17210840	77	TRDMT_HUMAN	59-84	26	1	A:59-78	20
1.10	ENST00000377799	10	ENSE00001695747	chr10:17204236-17204165	72	TRDMT_HUMAN	84-108	25	1	A:97-108	12
1.11	ENST00000377799	11	ENSE00001676885	chr10:17203547-17203482	66	TRDMT_HUMAN	108-130	23	1	A:108-130	23
1.12	ENST00000377799	12	ENSE00001706222	chr10:17202373-17202304	70	TRDMT_HUMAN	130-153	24	1	A:130-153	24
1.13b	ENST00000377799	13b	ENSE00001756222	chr10:17201228-17201145	84	TRDMT_HUMAN	154-181	28	1	A:154-181	28
1.14b	ENST00000377799	14b	ENSE00001726563	chr10:17199783-17199440	344	TRDMT_HUMAN	182-296	115	1	A:182-296 (gaps)	115
1.15	ENST00000377799	15	ENSE00001652345	chr10:17196733-17196676	58	TRDMT_HUMAN	296-315	20	1	A:296-315	20
1.16a	ENST00000377799	16a	ENSE00001612374	chr10:17195635-17195506	130	TRDMT_HUMAN	316-359	44	1	A:316-359	44
1.18e	ENST00000377799	18e	ENSE00001935652	chr10:17191139-17188736	2404	TRDMT_HUMAN	359-391	33	1	A:359-391	33

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:313
 aligned with TRDMT_HUMAN | O14717 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
          TRDMT_HUMAN     2 EPLRVLELYSGVGGMHHALRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGITLEEFDRLSFDMILMSPPCQPFTRIGRQGDMTDSRTNSFLHILDILPRLQKLPKYILLENVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEFPKIESVHPQKYAMDVENKIQEKNVEPNISFDGSIQCSGKDAILFKLETAEEIHRKNQQDSDLSVKMLKDFLEDDTDVNQYLLPPKSLLRYALLLDIVQPTCRRSVCFTKGYGSYIEGTGSVLQTAEDVQVENIYKSLTNLSQEEQITKLLILKLRYFTPKEIANLLGFPPEFGFPEKITVKQRYRLLGNSLNVHVVAKLIKILYE 391
               SCOP domains d1g55a_ A: DNMT2                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1g55A02 A:2-186,A:378-391 Vaccinia Virus protein VP39                                                                                                                                    1g                                                           55A01 A:187-377 DNA Methylase, subunit A, domain 2                                                                                1g55A02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh....ee..hhhhhhhhhhhhhh..eeee...------------------hhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeehhhhhh......eeeeeeee............ee.....-----------------------------------------------------------....hhhhhh....hhhhhh.hhhhhhhhhhhh.ee.......................eee.....hhhhhhhh....hhhhhhhhhhh..ee..hhhhhhhhh............hhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --SAM_MT_C5  PDB: A:4-391 UniProt: 4-391                                                                                                                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         -- PROSITE (2)
           Transcript 1 (1) Exon 1.1d  PDB: A:2-2-------------------------------------------------------------Exon 1.10  PDB: A:97-108 ---------------------Exon 1.12  PDB: A:130-15Exon 1.13b  PDB: A:154-181  Exon 1.14b  PDB: A:182-296 (gaps) UniProt: 182-296                                                                 -------------------Exon 1.16a  PDB: A:316-359 UniProt: 316-359 -------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.4b  PDB: A:22-58              Exon 1.9  PDB: A:59-78    -----------------------Exon 1.11              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.15           -------------------------------------------Exon 1.18e  PDB: A:359-391        Transcript 1 (2)
                 1g55 A   2 EPLRVLELYSGVGGMHHALRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGITLEEFDRLSFDMILMSPP------------------NSFLHILDILPRLQKLPKYILLENVKGFEVSSTRDLLIQTIENcGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEFPK-----------------------------------------------------------LSVKMLKDFLEDDTDVNQYLLPPKSLLRYALLLDIVQPTcRRSVCFTKGYGSYIEGTGSVLQTAEDVQVENIYKSLTNLSQEEQITKLLILKLRYFTPKEIANLLGFPPEFGFPEKITVKQRYRLLGNSLNVHVVAKLIKILYE 391
                                    11        21        31        41        51        61        71      |  -         -     | 101       111       121       131       141       151       161       171       181      |  -         -         -         -         -         -      |251       261       271       281     | 291       301       311       321       331       341       351       361       371       381       391
                                                                                                       78                 97                                        140-CSO                                         188                                                         248                                    287-CSO

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: C5 cytosine-specific DNA methylase, DCM (32)

Protein domain: DNMT2 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1g55a_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

1g55A02

A:2-186,A:378-391

Architecture: Alpha-Beta Complex (3881)

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

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

Human (Homo sapiens) (1)

1g55A01

A:187-377

(no "Pfam Domain" information available for 1G55)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRDMT_HUMAN | O14717)

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:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016428	tRNA (cytosine-5-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine.
	GO:0008175	tRNA methyltransferase activity	Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA 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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0001975	response to amphetamine	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 an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
	GO:0030488	tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
	GO:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	1g55
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (11, 11)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (15, 15)

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