1F3L - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CONSERVED CORE OF PROTEIN ARGININE METHYLTRANSFERASE PRMT3

Authors :   X. Zhang, L. Zhou, X. Cheng

Date :   05 Jun 00 (Deposition) - 14 Mar 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Beta Barrel, Rossmann Fold, Arginine Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhang, L. Zhou, X. Cheng
Crystal Structure Of The Conserved Core Of Protein Arginine Methyltransferase Prmt3.
Embo J. V. 19 3509 2000
PubMed-ID: 10899106 | Reference-DOI: 10.1093/EMBOJ/19.14.3509

Molecule 1 - PROTEIN ARGININE METHYLTRANSFERASE PRMT3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:4 , HOH A:42 , HOH A:43 , HOH A:51 , PHE A:218 , TYR A:221 , MET A:230 , ARG A:236 , GLY A:260 , CYS A:261 , ILE A:265 , ASP A:282 , GLN A:283 , SER A:284 , GLY A:308 , LYS A:309 , ILE A:310 , GLU A:311 , GLU A:326 , MET A:337 , SER A:340	BINDING SITE FOR RESIDUE SAH A 529

(no "SS Bond" information available for 1F3L)

Asymmetric Unit

No.	Residues
1	Tyr A:356	-	Pro A:357

(no "SAP(SNP)/Variant" information available for 1F3L)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_PRMT	PS51678	SAM-dependent methyltransferase PRMT-type domain profile.	ANM3_RAT	214-528	1	A:214-528

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_PRMT	PS51678	SAM-dependent methyltransferase PRMT-type domain profile.	ANM3_RAT	214-528	1	A:214-528

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_PRMT	PS51678	SAM-dependent methyltransferase PRMT-type domain profile.	ANM3_RAT	214-528	2	A:214-528

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000020853	1	ENSRNOE00000142108	chr1:99581943-99582048	106	ANM3_RAT	1-9	9	0	-	-
1.2	ENSRNOT00000020853	2	ENSRNOE00000148426	chr1:99582124-99582256	133	ANM3_RAT	9-53	45	0	-	-
1.3	ENSRNOT00000020853	3	ENSRNOE00000148514	chr1:99583892-99583974	83	ANM3_RAT	53-81	29	0	-	-
1.4	ENSRNOT00000020853	4	ENSRNOE00000143108	chr1:99584695-99584744	50	ANM3_RAT	81-97	17	0	-	-
1.5	ENSRNOT00000020853	5	ENSRNOE00000143322	chr1:99585945-99586047	103	ANM3_RAT	98-132	35	0	-	-
1.6	ENSRNOT00000020853	6	ENSRNOE00000143590	chr1:99590033-99590192	160	ANM3_RAT	132-185	54	0	-	-
1.7	ENSRNOT00000020853	7	ENSRNOE00000143836	chr1:99591278-99591419	142	ANM3_RAT	185-232	48	1	A:208-232	25
1.8	ENSRNOT00000020853	8	ENSRNOE00000144052	chr1:99594339-99594404	66	ANM3_RAT	233-254	22	1	A:233-254	22
1.9	ENSRNOT00000020853	9	ENSRNOE00000144266	chr1:99602460-99602581	122	ANM3_RAT	255-295	41	1	A:255-295	41
1.10	ENSRNOT00000020853	10	ENSRNOE00000144489	chr1:99610485-99610584	100	ANM3_RAT	295-328	34	1	A:295-328	34
1.11	ENSRNOT00000020853	11	ENSRNOE00000144706	chr1:99622500-99622578	79	ANM3_RAT	329-355	27	1	A:329-355	27
1.12	ENSRNOT00000020853	12	ENSRNOE00000341883	chr1:99631010-99631201	192	ANM3_RAT	355-419	65	1	A:355-419	65
1.13	ENSRNOT00000020853	13	ENSRNOE00000145291	chr1:99633153-99633247	95	ANM3_RAT	419-450	32	1	A:419-450	32
1.14	ENSRNOT00000020853	14	ENSRNOE00000145539	chr1:99656937-99656987	51	ANM3_RAT	451-467	17	1	A:451-467	17
1.15	ENSRNOT00000020853	15	ENSRNOE00000148623	chr1:99657179-99657266	88	ANM3_RAT	468-497	30	1	A:468-497	30
1.16	ENSRNOT00000020853	16	ENSRNOE00000148749	chr1:99667710-99668610	901	ANM3_RAT	497-532	36	1	A:497-528	32

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:321
 aligned with ANM3_RAT | O70467 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:321
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527 
             ANM3_RAT   208 DLQEDEDGVYFSSYGHYGIHEEMLKDKVRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAKAGAKKVIAVDQSEILYQAMDIIRLNKLEDTIVLIKGKIEEVSLPVEKVDVIISEWMGYFLLFESMLDSVLYAKSKYLAKGGSVYPDICTISLVAVSDVSKHADRIAFWDDVYGFNMSCMKKAVIPEAVVEVVDHKTLISDPCDIKHIDCHTTSISDLEFSSDFTLRTTKTAMCTAVAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTIFLLEKPFPVKAGEALKGKITVHKNKKDPRSLIVTLTLNSSTQTYSLQ 528
               SCOP domains d1f3la_ A: Arginine methyltransferase, HMT1                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------1f3lA01 A:215-357 Vaccinia Virus protein VP39                                                                                                  -1f3lA02 A:359-528 Hnrnp arginine n-methyltransferase1                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh.....eeeee............eeeee...........hhhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhh.....hhhhhhhh....eee..hhhh.....eeeeeee....hhhhhheeeeeeee....eeeeeeeeeeeeee.......eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SAM_MT_PRMT  PDB: A:214-528 UniProt: 214-528                                                                                                                                                                                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:208-232 Exon 1.8              ----------------------------------------Exon 1.10  PDB: A:295-328         Exon 1.11  PDB: A:329-355  ---------------------------------------------------------------Exon 1.13  PDB: A:419-450       Exon 1.14        Exon 1.15  PDB: A:468-497     ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.9  PDB: A:255-295 UniProt: 255-295-----------------------------------------------------------Exon 1.12  PDB: A:355-419 UniProt: 355-419                       -----------------------------------------------------------------------------Exon 1.16  PDB: A:497-528        Transcript 1 (2)
                 1f3l A 208 DLQEDEDGVYFSSYGHYGIHEEMLKDKVRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAKAGAKKVIAVDQSEILYQAMDIIRLNKLEDTIVLIKGKIEEVSLPVEKVDVIISEWMGYFLLFESMLDSVLYAKSKYLAKGGSVYPDICTISLVAVSDVSKHADRIAFWDDVYGFNMSCMKKAVIPEAVVEVVDHKTLISDPCDIKHIDCHTTSISDLEFSSDFTLRTTKTAMCTAVAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTIFLLEKPFPVKAGEALKGKITVHKNKKDPRSLIVTLTLNSSTQTYSLQ 528
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Norway rat (Rattus norvegicus) (23)

1f3lA01

A:215-357

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Hnrnp arginine n-methyltransferase1 (6)

Homologous Superfamily: Hnrnp arginine n-methyltransferase1 (6)

Norway rat (Rattus norvegicus) (4)

1f3lA02

A:359-528

(no "Pfam Domain" information available for 1F3L)

Asymmetric Unit(hide GO term definitions)

Chain A (ANM3_RAT | O70467)

molecular function
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
	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:0072341	modified amino acid binding	Interacting selectively and non-covalently with a modified amino acid.
	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:0060997	dendritic spine morphogenesis	The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
	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:0018216	peptidyl-arginine methylation	The addition of a methyl group to 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.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (10, 10)

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