3RJW - JenaLib

Title :   CRYSTAL STRUCTURE OF HISTONE LYSINE METHYLTRANSFERASE G9A WITH AN INHIBITOR

Authors :   A. Dong, G. A. Wasney, W. Tempel, F. Liu, D. Barsyte, A. Allali-Hassani, I. Chau, T. Hajian, G. Senisterra, N. Chavda, K. Arora, A. Siarheyeva, D. B. Kireev, J. M. Herold, A. Bochkarev, C. Bountra, J. Weigelt, A. M. E S. V. Frye, C. H. Arrowsmith, P. J. Brown, J. Jin, M. Vedadi, Structural Consortium (Sgc)

Date :   15 Apr 11 (Deposition) - 04 May 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.56

Chains :   Asym./Biol. Unit : A,B

Keywords :   Chemical Probe, Methyltransferase Inhibitor, Structural Genomics Consortium, Sgc, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Vedadi, D. Barsyte-Lovejoy, F. Liu, S. Rival-Gervier, A. Allali-Hassani, V. Labrie, T. J. Wigle, P. A. Dimaggio, G. A. Wasney A. Siarheyeva, A. Dong, W. Tempel, S. C. Wang, X. Chen, I. Chau, T. J. Mangano, X. P. Huang, C. D. Simpson, S. G. Pattenden, J. L. Norris, D. B. Kireev, A. Tripathy, A. Edwards, B. L. Roth, W. P. Janzen, B. A. Garcia, A. Petronis, J. Ellis, P. J. Brown, S. V. Frye, C. H. Arrowsmith, J. Jin
A Chemical Probe Selectively Inhibits G9A And Glp Methyltransferase Activity In Cells.
Nat. Chem. Biol. V. 7 566 2011
PubMed-ID: 21743462 | Reference-DOI: 10.1038/NCHEMBIO.599

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 41)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:974 , CYS A:987 , CYS A:1017 , CYS A:1021	BINDING SITE FOR RESIDUE ZN A 1394
02	AC2	SOFTWARE	CYS A:980 , CYS A:1017 , CYS A:1023 , CYS A:1027	BINDING SITE FOR RESIDUE ZN A 1395
03	AC3	SOFTWARE	CYS A:974 , CYS A:976 , CYS A:980 , CYS A:985	BINDING SITE FOR RESIDUE ZN A 1396
04	AC4	SOFTWARE	CYS A:1115 , CYS A:1168 , CYS A:1170 , CYS A:1175	BINDING SITE FOR RESIDUE ZN A 1397
05	AC5	SOFTWARE	HOH A:2 , MET A:1048 , TRP A:1050 , SER A:1084 , TYR A:1085 , ARG A:1109 , PHE A:1110 , ASN A:1112 , HIS A:1113 , TYR A:1154 , PHE A:1158 , PHE A:1166 , THR A:1167 , CYS A:1168 , GLN A:1169	BINDING SITE FOR RESIDUE SAH A 1198
06	AC6	SOFTWARE	TYR A:1067 , ASP A:1074 , ALA A:1077 , ASP A:1078 , ARG A:1080 , ASP A:1083 , SER A:1084 , LEU A:1086 , ASP A:1088 , TYR A:1154 , PHE A:1158 , ILE A:1161	BINDING SITE FOR RESIDUE CIQ A 2000
07	AC7	SOFTWARE	CYS B:974 , CYS B:987 , CYS B:1017 , CYS B:1021	BINDING SITE FOR RESIDUE ZN B 1394
08	AC8	SOFTWARE	CYS B:980 , CYS B:1017 , CYS B:1023 , CYS B:1027	BINDING SITE FOR RESIDUE ZN B 1395
09	AC9	SOFTWARE	CYS B:974 , CYS B:976 , CYS B:980 , CYS B:985	BINDING SITE FOR RESIDUE ZN B 1396
10	BC1	SOFTWARE	CYS B:1115 , CYS B:1168 , CYS B:1170 , CYS B:1175	BINDING SITE FOR RESIDUE ZN B 1397
11	BC2	SOFTWARE	MET B:1048 , TRP B:1050 , SER B:1084 , TYR B:1085 , ARG B:1109 , PHE B:1110 , ASN B:1112 , HIS B:1113 , TYR B:1154 , PHE B:1158 , PHE B:1166 , THR B:1167 , CYS B:1168 , GLN B:1169 , HOH B:1197	BINDING SITE FOR RESIDUE SAH B 1198
12	BC3	SOFTWARE	TYR B:1067 , ASP B:1074 , ALA B:1077 , ASP B:1078 , ARG B:1080 , ASP B:1083 , SER B:1084 , LEU B:1086 , ASP B:1088 , TYR B:1154 , PHE B:1158	BINDING SITE FOR RESIDUE CIQ B 2000

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (2, 4)

Exons (8, 16)

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.62b	ENST00000383373	62b	ENSE00001868068	HSCHR6_MHC_QBL:31855870-31855807	64	EHMT2_HUMAN	1-14	14	0	-	-
1.64e	ENST00000383373	64e	ENSE00001706010	HSCHR6_MHC_QBL:31855160-31855094	67	EHMT2_HUMAN	15-37	23	0	-	-
1.65a	ENST00000383373	65a	ENSE00001599572	HSCHR6_MHC_QBL:31854995-31854777	219	EHMT2_HUMAN	37-110	74	0	-	-
1.65e	ENST00000383373	65e	ENSE00001775009	HSCHR6_MHC_QBL:31854687-31854434	254	EHMT2_HUMAN	110-194	85	0	-	-
1.68i	ENST00000383373	68i	ENSE00001728907	HSCHR6_MHC_QBL:31851081-31850997	85	EHMT2_HUMAN	195-223	29	0	-	-
1.68j	ENST00000383373	68j	ENSE00001788063	HSCHR6_MHC_QBL:31850905-31850865	41	EHMT2_HUMAN	223-236	14	0	-	-
1.68m	ENST00000383373	68m	ENSE00001596027	HSCHR6_MHC_QBL:31850733-31850578	156	EHMT2_HUMAN	237-288	52	0	-	-
1.72f	ENST00000383373	72f	ENSE00001688918	HSCHR6_MHC_QBL:31847773-31847639	135	EHMT2_HUMAN	289-333	45	0	-	-
1.73	ENST00000383373	73	ENSE00001675787	HSCHR6_MHC_QBL:31847513-31847399	115	EHMT2_HUMAN	334-372	39	0	-	-
1.74a	ENST00000383373	74a	ENSE00001783494	HSCHR6_MHC_QBL:31847241-31847140	102	EHMT2_HUMAN	372-406	35	0	-	-
1.74e	ENST00000383373	74e	ENSE00001756695	HSCHR6_MHC_QBL:31846918-31846770	149	EHMT2_HUMAN	406-455	50	0	-	-
1.74g	ENST00000383373	74g	ENSE00001659464	HSCHR6_MHC_QBL:31846677-31846534	144	EHMT2_HUMAN	456-503	48	0	-	-
1.75d	ENST00000383373	75d	ENSE00001776567	HSCHR6_MHC_QBL:31846447-31846212	236	EHMT2_HUMAN	504-582	79	0	-	-
1.75e	ENST00000383373	75e	ENSE00001616295	HSCHR6_MHC_QBL:31846132-31845950	183	EHMT2_HUMAN	582-643	62	0	-	-
1.75f	ENST00000383373	75f	ENSE00001626945	HSCHR6_MHC_QBL:31845830-31845748	83	EHMT2_HUMAN	643-671	29	0	-	-
1.76b	ENST00000383373	76b	ENSE00001661306	HSCHR6_MHC_QBL:31845272-31845166	107	EHMT2_HUMAN	671-706	36	0	-	-
1.76d	ENST00000383373	76d	ENSE00001674057	HSCHR6_MHC_QBL:31845068-31844946	123	EHMT2_HUMAN	707-747	41	0	-	-
1.77b	ENST00000383373	77b	ENSE00001779819	HSCHR6_MHC_QBL:31844853-31844752	102	EHMT2_HUMAN	748-781	34	0	-	-
1.78k	ENST00000383373	78k	ENSE00001761048	HSCHR6_MHC_QBL:31843187-31843083	105	EHMT2_HUMAN	782-816	35	0	-	-
1.78q	ENST00000383373	78q	ENSE00001617974	HSCHR6_MHC_QBL:31842970-31842816	155	EHMT2_HUMAN	817-868	52	0	-	-
1.78t	ENST00000383373	78t	ENSE00001680216	HSCHR6_MHC_QBL:31842730-31842563	168	EHMT2_HUMAN	868-924	57	2	A:918-924 B:921-924	7 4
1.79h	ENST00000383373	79h	ENSE00001760590	HSCHR6_MHC_QBL:31842121-31841977	145	EHMT2_HUMAN	924-972	49	2	A:924-972 B:924-972	49 49
1.80b	ENST00000383373	80b	ENSE00001750625	HSCHR6_MHC_QBL:31841610-31841533	78	EHMT2_HUMAN	973-998	26	2	A:973-998 B:973-998	26 26
1.80c	ENST00000383373	80c	ENSE00001653707	HSCHR6_MHC_QBL:31841180-31841065	116	EHMT2_HUMAN	999-1037	39	2	A:999-1037 B:999-1037	39 39
1.80d	ENST00000383373	80d	ENSE00001641889	HSCHR6_MHC_QBL:31840956-31840870	87	EHMT2_HUMAN	1037-1066	30	2	A:1037-1066 B:1037-1066	30 30
1.83d	ENST00000383373	83d	ENSE00001692473	HSCHR6_MHC_QBL:31839264-31839186	79	EHMT2_HUMAN	1066-1092	27	2	A:1066-1092 B:1066-1091	27 26
1.84b	ENST00000383373	84b	ENSE00001740322	HSCHR6_MHC_QBL:31839020-31838845	176	EHMT2_HUMAN	1093-1151	59	2	A:1093-1151 B:1095-1151	59 57
1.86b	ENST00000383373	86b	ENSE00001647961	HSCHR6_MHC_QBL:31838436-31837931	506	EHMT2_HUMAN	1151-1210	60	2	A:1151-1187 (gaps) B:1151-1193	37 43

Sequences/Alignments

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:268
 aligned with EHMT2_HUMAN | Q96KQ7 from UniProtKB/Swiss-Prot  Length:1210

    Alignment length:270
                                   927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187
         EHMT2_HUMAN    918 TEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQS 1187
               SCOP domains d3rjwa_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.............eee...........ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eeeee.....eeeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhh--.............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F---------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------PRE_SET  PDB: A:972-1035 UniProt: 972-1035                      --SET  PDB: A:1038-1155 UniProt: 1038-1155                                                                              -------------------------------- PROSITE
           Transcript 1 (1) 1.78t  ------------------------------------------------Exon 1.80b  PDB: A:973-998Exon 1.80c  PDB: A:999-1037            ----------------------------Exon 1.83d  PDB: A:1066-109Exon 1.84b  PDB: A:1093-1151 UniProt: 1093-1151            ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.79h  PDB: A:924-972 UniProt: 924-972      ----------------------------------------------------------------Exon 1.80d  PDB: A:1037-1066  ------------------------------------------------------------------------------------Exon 1.86b  PDB: A:1151-1187 (gaps)   Transcript 1 (2)
                3rjw A  918 TEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIK--YFTCQCGSEKCKHSAEAIALEQS 1187
                                   927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157    | 1167      1177      1187
                                                                                                                                                                                                                                                                             1162  |                      
                                                                                                                                                                                                                                                                                1165

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with EHMT2_HUMAN | Q96KQ7 from UniProtKB/Swiss-Prot  Length:1210

    Alignment length:273
                                   930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190   
         EHMT2_HUMAN    921 IICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLARLD 1193
               SCOP domains d3rjwb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Pre-SET-3rjwB01 B:925-1030                                                                                ------------------SET-3rjwB03 B:1049-1155                                                                                    -------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Pre-SET-3rjwB02 B:925-1030                                                                                ------------------SET-3rjwB04 B:1049-1155                                                                                    -------------------------------------- Pfam domains (2)
         Sec.struct. author ................ee............ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eeee..---..eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------PRE_SET  PDB: B:972-1035 UniProt: 972-1035                      --SET  PDB: B:1038-1155 UniProt: 1038-1155                                                                              -------------------------------------- PROSITE
           Transcript 1 (1) 1.78------------------------------------------------Exon 1.80b  PDB: B:973-998Exon 1.80c  PDB: B:999-1037            ----------------------------Exon 1.83d  PDB: B:1066-109Exon 1.84b  PDB: B:1095-1151 UniProt: 1093-1151            ------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.79h  PDB: B:924-972 UniProt: 924-972      ----------------------------------------------------------------Exon 1.80d  PDB: B:1037-1066  ------------------------------------------------------------------------------------Exon 1.86b  PDB: B:1151-1193 [INCOMPLETE]   Transcript 1 (2)
                3rjw B  921 IICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDN---EVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLARLD 1193
                                   930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090|   | 1100      1110      1120      1130      1140      1150      1160      1170      1180      1190   
                                                                                                                                                                                                   1091   |                                                                                                  
                                                                                                                                                                                                       1095

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (EHMT2_HUMAN | Q96KQ7)

molecular function
	GO:0070742	C2H2 zinc finger domain binding	Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
	GO:0046976	histone methyltransferase activity (H3-K27 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group onto lysine at position 27 of the histone H3 protein.
	GO:0046974	histone methyltransferase activity (H3-K9 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 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: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:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of proteins.
	GO:1990841	promoter-specific chromatin binding	Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA.
	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:0016279	protein-lysine N-methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0009267	cellular response to starvation	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 deprivation of nourishment.
	GO:0070734	histone H3-K27 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone.
	GO:0051567	histone H3-K9 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
	GO:0034968	histone lysine methylation	The modification of a histone by addition of one or more methyl groups to a lysine residue.
	GO:0016571	histone methylation	The modification of histones by addition of methyl groups.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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:0018027	peptidyl-lysine dimethylation	The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	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.

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Description