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Title :   CRYSTAL STRUCTURE OF HUMAN SET DOMAIN-CONTAINING PROTEIN3

Authors :   A. Dong, H. Zeng, J. R. Walker, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min, H. Wu, Structural Genomics C (Sgc)

Date :   28 Jun 11 (Deposition) - 20 Jul 11 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Setd3, Histone Methyltransferase, Histone Modification, Lysine, Post- Translational Modification, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zeng, A. Dong, J. R. Walker, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min, H. Wu
Crystal Structure Of Human Set Domain-Containing Protein3
To Be Published
PubMed: search

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD3
	Chains	:	A
	EC Number	:	2.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21 (DE3)V2RPRARE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SETD3, C14ORF154
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SET DOMAIN-CONTAINING PROTEIN 3

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 27)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ARS	2	Ligand/Ion	ARSENIC
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE
6	UNX	11	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (6, 27)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ARS	2	Ligand/Ion	ARSENIC
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE
6	UNX	11	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (6, 54)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	ARS	4	Ligand/Ion	ARSENIC
3	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
5	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE
6	UNX	22	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:74 , GLU A:102 , GLU A:103 , PHE A:105 , THR A:252 , ARG A:253 , ASP A:274 , MSE A:275 , CYS A:276 , ASN A:277 , HIS A:278 , TYR A:312 , SER A:324 , PHE A:326 , PHE A:328 , HOH A:515 , HOH A:545 , HOH A:569 , HOH A:603 , HOH A:762 , HOH A:794	BINDING SITE FOR RESIDUE SAM A 1000
2	AC2	SOFTWARE	CYS A:296	BINDING SITE FOR RESIDUE ARS A 498
3	AC3	SOFTWARE	CYS A:294	BINDING SITE FOR RESIDUE ARS A 499
4	AC4	SOFTWARE	PHE A:100 , ARG A:108 , GLY A:305 , GLU A:306 , GLN A:307 , ASP A:455 , HOH A:525 , HOH A:718	BINDING SITE FOR RESIDUE PG4 A 4001
5	AC5	SOFTWARE	PHE A:367 , ALA A:368 , SER A:377 , GLN A:379 , HOH A:753 , HOH A:789	BINDING SITE FOR RESIDUE ACT A 500
6	AC6	SOFTWARE	LEU A:340 , GLY A:341 , PHE A:387 , PHE A:428 , ARG A:432 , HOH A:655	BINDING SITE FOR RESIDUE ACT A 1001

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

Asymmetric Unit

No.	Residues
1	Glu A:373	-	Pro A:374

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028830	N	278	D	SETD3_HUMAN	Polymorphism	1740231	A	N	277	D

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028830	N	278	D	SETD3_HUMAN	Polymorphism	1740231	A	N	277	D

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028830	N	278	D	SETD3_HUMAN	Polymorphism	1740231	A	N	277	D

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SETD3_HUMAN	94-314	1	A:93-313

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SETD3_HUMAN	94-314	1	A:93-313

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	SETD3_HUMAN	94-314	2	A:93-313

(no "Exon" information available for 3SMT)

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:465
 aligned with SETD3_HUMAN | Q86TU7 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:473
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490   
          SETD3_HUMAN    21 SPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEKIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEELFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSFTYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAVKSAAVNREYYRQQM 493
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....----hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh......eeeeee...eeeeee........eeeeee.hhheehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh----...........hhhhhhhhhhhhhhhheeee......eeeee..hhhhhee....eeeeee....eeeeee........eeee.....hhhhhhhhhh.........eeeeeee......hhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhh.hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------SET  PDB: A:93-313 UniProt: 94-314                                                                                                                                                                                           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3smt A  20 SPKEILNLTSELLQKCSSPA----KEWEEYVQIRTLVEKIRKKQKGLSVTFDGKREDYFPDLmKWASENGASVEGFEmVNFKEEGFGLRATRDIKAEELFLWVPRKLLmTVESAKNSVLGPLYSQDRILQAmGNIALAFHLLCERASPNSFWQPYIQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVI----HANKLPLKDSFTYEDYRWAVSSVmTRQNQIPTEDGSRVTLALIPLWDmCNHTNGLITTGYNLEDDRCECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAmKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCmTEEELKEHLLGDSAIDRIFTLGNSEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKmAIKLRLGEKEILEKAVKSAAVNREYYRQQm 492
                                    29        39    |   49        59        69        79  |     89       |99       109       119       129       139       149 |     159       169       179       189       199       209       219   |   229       239       249 |     259       269     | 279       289       299       309       319       329       339       349 |     359       369       379       389       399       409       419       429       439       449       459  |    469       479       489  |
                                              39   44                                    82-MSE         97-MSE                        128-MSE                151-MSE                                                                 223  228                    251-MSE                 275-MSE                                                                     351-MSE                               389-MSE                                                                  462-MSE                       492-MSE

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	-	→ 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 3SMT)

(no "CATH Domain" information available for 3SMT)

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

Asymmetric Unit(hide GO term definitions)

Chain A (SETD3_HUMAN | Q86TU7)

molecular function
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	GO:0046975	histone methyltransferase activity (H3-K36 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group onto lysine at position 36 of the histone H3 protein.
	GO:0042800	histone methyltransferase activity (H3-K4 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
	GO:0018024	histone-lysine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating 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:0010452	histone H3-K36 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone.
	GO:0051568	histone H3-K4 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0018027	peptidyl-lysine dimethylation	The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
	GO:0018022	peptidyl-lysine methylation	The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative.
	GO:0018026	peptidyl-lysine monomethylation	The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
	GO:0018023	peptidyl-lysine trimethylation	The methylation of peptidyl-lysine to form peptidyl-N6,N6,N6-trimethyl-L-lysine.
	GO:0051149	positive regulation of muscle cell differentiation	Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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 Unit
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	Cis Peptide Bonds
		Glu A:373 - Pro A:374	[ RasMol ]

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	3smt
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	SETD3_HUMAN \| Q86TU7
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	2.1.1.43
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (6, 27)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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