3EPP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MRNA CAP GUANINE-N7 METHYLTRANSFERASE (RNMT) IN COMPLEX WITH SINEFUNGIN

Authors :   M. F. Amaya, H. Zeng, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmit A. M. Edwards, A. Botchkarev, J. Min, A. N. Plotnikov, H. Wu, Structura Genomics Consortium (Sgc)

Date :   29 Sep 08 (Deposition) - 21 Oct 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.41

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

Keywords :   Mrna Cap Guanine-N7 Methyltransferase, Rnmt, Sinefungin, Structural Genomics, Structural Genomics Consortium, Sgc, Mrna Capping, Mrna Processing, Nucleus, Phosphoprotein, Rna-Binding, S-Adenosyl-L- Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zeng, M. F. Amaya, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Botchkarev, J. Min, A. N. Plotnikov H. Wu
Crystal Structure Of Mrna Cap Guanine-N7 Methyltransferase (Rnmt) In Complex With Sinefungin.
To Be Published
PubMed: search

Molecule 1 - MRNA CAP GUANINE-N7 METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.56
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	DH5A
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 165-476
	Gene	:	RNMT, KIAA0398
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MRNA (GUANINE-N(7)-)-METHYLTRANSFERASE, RG7MT1, MRNA CAP METHYLTRANSFERASE, HCM1P, HCMT1, HMET

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SFG	2	Ligand/Ion	SINEFUNGIN

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SFG	1	Ligand/Ion	SINEFUNGIN

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SFG	1	Ligand/Ion	SINEFUNGIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:17 , GLY A:42 , GLY A:44 , ASP A:64 , ILE A:65 , ASP A:98 , SER A:99 , SER A:100 , GLN A:121 , PHE A:122 , VAL A:123 , TYR A:126 , MET A:137 , HOH A:427 , HOH A:444	BINDING SITE FOR RESIDUE SFG A 401
2	AC2	SOFTWARE	LYS B:17 , GLY B:42 , GLY B:44 , ASP B:64 , ILE B:65 , ASP B:98 , SER B:99 , GLN B:121 , PHE B:122 , VAL B:123 , TYR B:126 , MET B:137 , HOH B:430 , HOH B:474	BINDING SITE FOR RESIDUE SFG B 401

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

(no "Cis Peptide Bond" information available for 3EPP)

(no "SAP(SNP)/Variant" information available for 3EPP)

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

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000383314	1	ENSE00001313973	chr18:13726660-13726728	69	MCES_HUMAN	-	0	0	-	-
1.2	ENST00000383314	2	ENSE00001540359	chr18:13730626-13730754	129	MCES_HUMAN	-	0	0	-	-
1.3b	ENST00000383314	3b	ENSE00001120461	chr18:13731475-13731933	459	MCES_HUMAN	1-139	139	0	-	-
1.4	ENST00000383314	4	ENSE00000666433	chr18:13734463-13734598	136	MCES_HUMAN	140-185	46	2	A:6-22 B:5-22	17 18
1.5	ENST00000383314	5	ENSE00000666434	chr18:13737009-13737134	126	MCES_HUMAN	185-227	43	2	A:22-64 (gaps) B:22-64	43 43
1.6	ENST00000383314	6	ENSE00000666435	chr18:13740166-13740278	113	MCES_HUMAN	227-264	38	2	A:64-101 (gaps) B:64-101 (gaps)	38 38
1.7	ENST00000383314	7	ENSE00000666436	chr18:13741509-13741690	182	MCES_HUMAN	265-325	61	2	A:102-162 B:102-162	61 61
1.8	ENST00000383314	8	ENSE00000666437	chr18:13742487-13742651	165	MCES_HUMAN	325-380	56	2	A:162-217 (gaps) B:162-217 (gaps)	56 56
1.9	ENST00000383314	9	ENSE00000666438	chr18:13746219-13746336	118	MCES_HUMAN	380-419	40	2	A:217-253 B:217-253	37 37
1.10	ENST00000383314	10	ENSE00000883621	chr18:13752325-13752426	102	MCES_HUMAN	420-453	34	2	A:288-290 B:288-290	3 3
1.11	ENST00000383314	11	ENSE00000883622	chr18:13754113-13754146	34	MCES_HUMAN	454-465	12	2	A:291-302 B:291-302	12 12
1.12b	ENST00000383314	12b	ENSE00001496033	chr18:13759941-13764557	4617	MCES_HUMAN	465-476	12	2	A:302-313 B:302-313	12 12

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:265
 aligned with MCES_HUMAN | O43148 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:308
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468        
           MCES_HUMAN   169 IFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQALEPYPANESSKLVSEKVDDYEHAAKYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEKQQ 476
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eppA00 A:6-313 Vaccinia Vi  rus protein VP39                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..--..eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh--.....eeeeee......hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhh...eee....eeee...........eeeee-----..eee..hhhhhhhhhh...eeeeeeeehhhhhhhhh.hhhhhhhhhhhh----------------------------------......hhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4         -----------------------------------------Exon 1.6  PDB: A:64-101 (gaps)        Exon 1.7  PDB: A:102-162 UniProt: 265-325                    ------------------------------------------------------Exon 1.9  PDB: A:217-253 [INCOMPLETE]   Exon 1.10  PDB: A:288-290         Exon 1.11   ----------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.5  PDB: A:22-64 (gaps)              -------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:162-217 (gaps) UniProt: 325-380        ------------------------------------------------------------------------------------Exon 1.12b   Transcript 1 (2)
                 3epp A   6 IFYLRNFNNWMKSVLIGEFLEKVRQKK--DITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNR--SEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFN-----DVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQ----------------------------------LPLGTLSKSEWEATSIYLVFAFEKQQ 313
                                    15        25      | 35        45        55        65        75       | -|       95       105       115       125       135       145       155       165       175       185       195  |    205       215       225       235       245       | -         -         -         -  |    295       305        
                                                     32 35                                              83 86                                                                                                             198   204                                              253                                288

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with MCES_HUMAN | O43148 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:309
                                   177       187       197       207       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         
           MCES_HUMAN   168 RIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQALEPYPANESSKLVSEKVDDYEHAAKYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEKQQ 476
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eppB00 B:5-313 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.----...eeeeee......hhhhh.......eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhh...eee...eeeee...........eeeeee.---..eee..hhhhhhhhhh...eeeeeeeehhhhhhhhh.hhhhhhhhhhhh----------------------------------......hhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4          -----------------------------------------Exon 1.6  PDB: B:64-101 (gaps)        Exon 1.7  PDB: B:102-162 UniProt: 265-325                    ------------------------------------------------------Exon 1.9  PDB: B:217-253 [INCOMPLETE]   Exon 1.10  PDB: B:288-290         Exon 1.11   ----------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.5  PDB: B:22-64 UniProt: 185-227    -------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:162-217 (gaps) UniProt: 325-380        ------------------------------------------------------------------------------------Exon 1.12b   Transcript 1 (2)
                 3epp B   5 RIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNR----YIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLE---DVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQ----------------------------------LPLGTLSKSEWEATSIYLVFAFEKQQ 313
                                    14        24        34        44        54        64        74        |-   |    94       104       114       124       134       144       154       164       174       184       194     | 204       214       224       234       244        |-         -         -         -   |   294       304         
                                                                                                         83   88                                                                                                             200 204                                              253                                288

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 "SCOP Domain" information available for 3EPP)

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)

Homo sapiens. Organism_taxid: 9606. (1)

1a	3eppA00	A:6-313
1b	3eppB00	B:5-313

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (MCES_HUMAN | O43148)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004482	mRNA (guanine-N7-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA. m7G(5')pppR-RNA is mRNA containing an N7-methylguanine cap; R may be guanosine or adenosine.
	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: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:0006370	7-methylguanosine mRNA capping	Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
	GO:0036265	RNA (guanine-N7)-methylation	The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
cellular component
	GO:0005845	mRNA cap binding complex	Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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	MCES_HUMAN \| O43148	:	3bgv 5e8j 5e9j 5e9w

3bgv	CRYSTAL STRUCTURE OF MRNA CAP GUANINE-N7 METHYLTRANSFERASE IN COMPLEX WITH SAH

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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Exons (9, 18)

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