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Title :   CRYSTAL STRUCTURE OF THE PWWP DOMAIN OF MAMMALIAN DNA METHYLTRANSFERASE DNMT3B

Authors :   C. Qiu, K. Sawada, X. Zhang, X. Cheng

Date :   29 Nov 01 (Deposition) - 27 Feb 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Five Beta-Sheets Barrel Followed By Five-Helix Bundle, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Qiu, K. Sawada, X. Zhang, X. Cheng
The Pwwp Domain Of Mammalian Dna Methyltransferase Dnmt3B Defines A New Family Of Dna-Binding Folds.
Nat. Struct. Biol. V. 9 217 2002
PubMed-ID: 11836534

Molecule 1 - DNA CYTOSINE-5 METHYLTRANSFERASE 3B2
	Chains	:	A
	EC Number	:	2.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PWWP DOMAIN (RESIDUES 219-365)
	Gene	:	DNMT3B
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 22)

No.	Name	Count	Type	Full Name
1	UNX	22	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	UNX A:164 , UNX A:165 , UNX A:166 , SER A:257	BINDING SITE FOR RESIDUE UNX A 163
02	AC2	SOFTWARE	UNX A:163 , UNX A:165 , UNX A:166 , PHE A:271 , GLY A:272	BINDING SITE FOR RESIDUE UNX A 164
03	AC3	SOFTWARE	UNX A:163 , UNX A:164 , UNX A:166 , SER A:257 , GLY A:274	BINDING SITE FOR RESIDUE UNX A 165
04	AC4	SOFTWARE	HOH A:40 , UNX A:163 , UNX A:164 , UNX A:165 , GLN A:269 , TRP A:270 , GLY A:274	BINDING SITE FOR RESIDUE UNX A 166
05	AC5	SOFTWARE	HOH A:100 , UNX A:168	BINDING SITE FOR RESIDUE UNX A 167
06	AC6	SOFTWARE	HOH A:61 , UNX A:167 , TRP A:342	BINDING SITE FOR RESIDUE UNX A 168
07	AC7	SOFTWARE	HOH A:103 , HOH A:120 , UNX A:170 , UNX A:171	BINDING SITE FOR RESIDUE UNX A 169
08	AC8	SOFTWARE	UNX A:169 , UNX A:171 , LYS A:348	BINDING SITE FOR RESIDUE UNX A 170
09	AC9	SOFTWARE	HOH A:88 , HOH A:100 , UNX A:169 , UNX A:170 , ALA A:297	BINDING SITE FOR RESIDUE UNX A 171
10	BC1	SOFTWARE	UNX A:173 , UNX A:174 , LYS A:315 , ARG A:319	BINDING SITE FOR RESIDUE UNX A 172
11	BC2	SOFTWARE	HOH A:121 , UNX A:172 , UNX A:174	BINDING SITE FOR RESIDUE UNX A 173
12	BC3	SOFTWARE	UNX A:172 , UNX A:173 , GLY A:233	BINDING SITE FOR RESIDUE UNX A 174
13	BC4	SOFTWARE	HOH A:7 , HOH A:130 , UNX A:176 , UNX A:177 , LYS A:315	BINDING SITE FOR RESIDUE UNX A 175
14	BC5	SOFTWARE	UNX A:175 , UNX A:177 , VAL A:318	BINDING SITE FOR RESIDUE UNX A 176
15	BC6	SOFTWARE	UNX A:175 , UNX A:176 , LYS A:315	BINDING SITE FOR RESIDUE UNX A 177
16	BC7	SOFTWARE	UNX A:179 , UNX A:181 , UNX A:182 , UNX A:183 , UNX A:184 , GLY A:288 , PHE A:290 , SER A:291 , GLN A:292	BINDING SITE FOR RESIDUE UNX A 178
17	BC8	SOFTWARE	HOH A:60 , UNX A:178 , UNX A:180 , UNX A:181 , ASP A:282 , GLN A:292	BINDING SITE FOR RESIDUE UNX A 179
18	BC9	SOFTWARE	HOH A:85 , HOH A:151 , UNX A:179 , UNX A:181 , UNX A:184 , GLY A:288	BINDING SITE FOR RESIDUE UNX A 180
19	CC1	SOFTWARE	UNX A:178 , UNX A:179 , UNX A:180 , UNX A:182 , UNX A:183 , UNX A:184 , ASP A:282	BINDING SITE FOR RESIDUE UNX A 181
20	CC2	SOFTWARE	UNX A:178 , UNX A:181 , UNX A:183 , UNX A:184 , ALA A:343 , GLY A:346	BINDING SITE FOR RESIDUE UNX A 182
21	CC3	SOFTWARE	UNX A:178 , UNX A:181 , UNX A:182 , ASP A:282 , SER A:291 , HIS A:344	BINDING SITE FOR RESIDUE UNX A 183
22	CC4	SOFTWARE	UNX A:178 , UNX A:180 , UNX A:181 , UNX A:182 , GLY A:288 , PHE A:347 , ILE A:352	BINDING SITE FOR RESIDUE UNX A 184

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:348	-	Pro A:349

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PWWP	PS50812	PWWP domain profile.	DNM3B_MOUSE	232-290	1	A:232-290

(no "Exon" information available for 1KHC)

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
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Chain A from PDB  Type:PROTEIN  Length:137
 aligned with DNM3B_MOUSE | O88509 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:137
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       
          DNM3B_MOUSE   222 TEYQDDKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMPGMRWVQWFGDGKFSEISADKLVALGLFSQHFNLATFNKLVSYRKAMYHTLEKARVRAGKTFSSSPGESLEDQLKPMLEWAHGGFKPTGIEGLKPN 358
               SCOP domains d1khca_ A: DNA methyltransferase DNMT3B                                                                                                   SCOP domains
               CATH domains -1khcA01 A:223-287  [code=2.30.30.160, no name defined]           1khcA02 A:288-356 PWWP, helical domain                               -- CATH domains
               Pfam domains -------PWWP-1khcA01 A:229-302                                                    -------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .............eeeeee...eeeeeeeehhhhh........eeeeee.....eeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------ee------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PWWP  PDB: A:232-290 UniProt: 232-290                      -------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khc A 222 TEYQDDKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMPGMRWVQWFGDGKFSEISADKLVALGLFSQHFNLATFNKLVSYRKAMYHTLEKARVRAGKTFSSSPGESLEDQLKPMLEWAHGGFKPTGIEGLKPN 358
                                   231       241       251       261       271       281       291       301       311       321       331       341       351

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: PWWP domain (14)

Protein domain: DNA methyltransferase DNMT3B (2)

Mouse (Mus musculus) [TaxId: 10090] (1)

d1khca_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 (23)

Homologous Superfamily: PWWP, helical domain (2)

House mouse (Mus musculus) (1)

1khcA02

A:288-356

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.160, no name defined] (35)

House mouse (Mus musculus) (2)

1khcA01

A:223-287

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tudor (88)

Family: PWWP (17)

Mus musculus (Mouse) (2)

PWWP-1khcA01

A:229-302

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DNM3B_MOUSE | O88509)

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:0051719	DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates	Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing CpN = S-adenosyl-L-homocysteine + DNA containing 5-MeCpN.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0009008	DNA-methyltransferase activity	Catalysis of the transfer of a methyl group to a DNA molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	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:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0043045	DNA methylation involved in embryo development	The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression.
	GO:0032776	DNA methylation on cytosine	The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
	GO:0071230	cellular response to amino acid 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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0060821	inactivation of X chromosome by DNA methylation	Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by a mechanism of DNA methylation.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006346	methylation-dependent chromatin silencing	Repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	GO:0051573	negative regulation of histone H3-K9 methylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:0031503	protein complex localization	A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006349	regulation of gene expression by genetic imprinting	Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.
cellular component
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	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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	Cis Peptide Bonds
		Lys A:348 - Pro A:349	[ RasMol ]

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	1khc
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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 22)

Sites (22, 22)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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