3SMQ - JenaLib

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Title :   CRYSTAL STRUCTURE OF PROTEIN ARGININE METHYLTRANSFERASE 3

Authors :   E. Dobrovetsky, A. Dong, J. R. Walker, A. Siarheyeva, G. Senisterra, G. D. Smil, Y. Bolshan, K. T. Nguyen, A. Allali-Hassani, T. Hajian, G. Pod C. Bountra, J. Weigelt, A. M. Edwards, R. Al-Awar, P. J. Brown, M. Schap C. H. Arrowsmith, M. Vedadi, Structural Genomics Consortium (Sgc

Date :   28 Jun 11 (Deposition) - 31 Aug 11 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Prmt3, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Siarheyeva, G. Senisterra, A. Allali-Hassani, A. Dong, E. Dobrovetsky, G. A. Wasney, I. Chau, R. Marcellus, T. Hajian, F. Liu, I. Korboukh, D. Smil, Y. Bolshan, J. Min, H. Wu, H. Zeng, P. Loppnau, G. Poda, C. Griffin, A. Aman, P. J. Brown, J. Jin, R. Al-Awar, C. H. Arrowsmith, M. Schapira, M. Vedadi
An Allosteric Inhibitor Of Protein Arginine Methyltransferase 3.
Structure V. 20 1425 2012
PubMed-ID: 22795084 | Reference-DOI: 10.1016/J.STR.2012.06.001

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 3
	Chains	:	A
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-LIC
	Expression System Strain	:	BL21(DE3)-V2R-PRAR2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 211-531
	Gene	:	PRMT3, HRMT1L3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN METHYLTRANSFERASE- LIKE PROTEIN 3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	TDU	1	Ligand/Ion	1-(1,2,3-BENZOTHIADIAZOL-6-YL)-3-[2-(CYCLOHEX-1-EN-1-YL)ETHYL]UREA
3	UNX	10	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 22)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	TDU	2	Ligand/Ion	1-(1,2,3-BENZOTHIADIAZOL-6-YL)-3-[2-(CYCLOHEX-1-EN-1-YL)ETHYL]UREA
3	UNX	20	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:245 , GLU A:248 , VAL A:387 , ASP A:389 , LYS A:392 , HIS A:393 , ARG A:396 , VAL A:420 , GLU A:422 , THR A:466 , ALA A:467	BINDING SITE FOR RESIDUE TDU A 1
2	AC2	SOFTWARE	SER A:388 , SER A:463 , MET A:464	BINDING SITE FOR RESIDUE CL A 1000

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

Asymmetric Unit

No.	Residues
1	Tyr A:376	-	Pro A:377

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024584	L	440	V	ANM3_HUMAN	Polymorphism	3758805	A	L	457	V
2	UniProt	VAR_030943	S	470	C	ANM3_HUMAN	Polymorphism	11025585	A	S	487	C

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

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024584	L	440	V	ANM3_HUMAN	Polymorphism	3758805	A	L	457	V
2	UniProt	VAR_030943	S	470	C	ANM3_HUMAN	Polymorphism	11025585	A	S	487	C

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

(no "PROSITE Motif" information available for 3SMQ)

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000331079	1a	ENSE00002150419	chr11:20409076-20409320	245	ANM3_HUMAN	1-10	10	0	-	-
1.1f	ENST00000331079	1f	ENSE00001293242	chr11:20409565-20409700	136	ANM3_HUMAN	10-55	46	0	-	-
1.2	ENST00000331079	2	ENSE00001797621	chr11:20411290-20411372	83	ANM3_HUMAN	55-83	29	0	-	-
1.3b	ENST00000331079	3b	ENSE00001297538	chr11:20413757-20413806	50	ANM3_HUMAN	83-99	17	0	-	-
1.4	ENST00000331079	4	ENSE00001314511	chr11:20414443-20414545	103	ANM3_HUMAN	100-134	35	0	-	-
1.6	ENST00000331079	6	ENSE00001291287	chr11:20417349-20417508	160	ANM3_HUMAN	134-187	54	0	-	-
1.7b	ENST00000331079	7b	ENSE00001318617	chr11:20419123-20419267	145	ANM3_HUMAN	187-235	49	1	A:243-252	10
1.8	ENST00000331079	8	ENSE00001314116	chr11:20424465-20424530	66	ANM3_HUMAN	236-257	22	1	A:253-274	22
1.9b	ENST00000331079	9b	ENSE00001290930	chr11:20429457-20429578	122	ANM3_HUMAN	258-298	41	1	A:275-315	41
1.10	ENST00000331079	10	ENSE00001318398	chr11:20448312-20448411	100	ANM3_HUMAN	298-331	34	1	A:315-348	34
1.11	ENST00000331079	11	ENSE00001294882	chr11:20473676-20473754	79	ANM3_HUMAN	332-358	27	1	A:349-375	27
1.12	ENST00000331079	12	ENSE00001311854	chr11:20483526-20483713	188	ANM3_HUMAN	358-420	63	1	A:375-437	63
1.13	ENST00000331079	13	ENSE00001327931	chr11:20486006-20486092	87	ANM3_HUMAN	421-449	29	1	A:438-466	29
1.14	ENST00000331079	14	ENSE00001291109	chr11:20515465-20515515	51	ANM3_HUMAN	450-466	17	1	A:467-483	17
1.15	ENST00000331079	15	ENSE00001310698	chr11:20515713-20515800	88	ANM3_HUMAN	467-496	30	1	A:484-513	30
1.16b	ENST00000331079	16b	ENSE00002195347	chr11:20529850-20530799	950	ANM3_HUMAN	496-531	36	1	A:513-547 (gaps)	35

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:299
 aligned with ANM3_HUMAN | O60678 from UniProtKB/Swiss-Prot  Length:531

    Alignment length:305
                                   235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525     
           ANM3_HUMAN   226 HYGIHEEMLKDKIRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAKAGAKKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVDVIISEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYPDICTISLVAVSDVNKHADRIAFWDDVYGFKMSCMKKAVIPEAVVEVLDPKTLISEPCGIKHIDCHTTSISDLEFSSDFTLKITRTSMCTAIAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTVFLLEKPFSVKAGEALKGKVTVHKSKKDPRSLTVTLTLNNSTQTYGL 530
               SCOP domains d3smqa_ A: Protein arginine N-methyltransferase 3, PRMT3                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee............eeeee............hhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhh.....hhhhhhhhh...eee..hhhhh....eeeeeee....hhhhhheeeeeeee....eeeeeeeeeeeeee.......eeee...........eeeeeeeeeeee....eeeeeeeee.------..eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------C------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7b Exon 1.8              ----------------------------------------Exon 1.10  PDB: A:315-348         Exon 1.11  PDB: A:349-375  --------------------------------------------------------------Exon 1.13  PDB: A:438-466    Exon 1.14        Exon 1.15  PDB: A:484-513     ---------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.9b  PDB: A:275-315                -----------------------------------------------------------Exon 1.12  PDB: A:375-437 UniProt: 358-420                     ---------------------------------------------------------------------------Exon 1.16b  PDB: A:513-547 (gaps)   Transcript 1 (2)
                 3smq A 243 HYGIHEEMLKDKIRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAKAGAKKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVDVIISEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYPDICTISLVAVSDVNKHADRIAFWDDVYGFKMSCMKKAVIPEAVVEVLDPKTLISEPCGIKHIDCHTTSISDLEFSSDFTLKITRTSMCTAIAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTVFLLEKPFSVKAGEALKGKVTVHK------SLTVTLTLNNSTQTYGL 547
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522 |     532       542     
                                                                                                                                                                                                                                                                                                                   524    531

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 '\|'

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (ANM3_HUMAN | O60678)

molecular function
	GO:0008469	histone-arginine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine.
	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:0016274	protein-arginine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine.
	GO:0035242	protein-arginine omega-N asymmetric methyltransferase activity	Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues.
	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:0034969	histone arginine methylation	The modification of a histone by addition of a methyl group to an arginine residue.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0031397	negative regulation of protein ubiquitination	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	GO:0035246	peptidyl-arginine N-methylation	The addition of a methyl group onto a nitrogen atom of an arginine residue in a protein.
	GO:0019919	peptidyl-arginine methylation, to asymmetrical-dimethyl arginine	The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine.
	GO:0006479	protein methylation	The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (10, 10)

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