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Asym./Biol. Unit (Jmol Viewer)

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Title :   WESSELSBRON VIRUS METHYLTRANSFERASE IN COMPLEX WITH ADOMET

Authors :   M. Bollati, S. Ricagno, M. Milani, E. Mastrangelo, M. Bolognesi

Date :   23 Sep 08 (Deposition) - 18 Nov 08 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Flavivirus, Rna Capping, Methyltransferase, Guanylyltransferase, Viral Enzyme Structure, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Bollati, M. Milani, E. Mastrangelo, S. Ricagno, G. Tedeschi, S. Nonnis, E. Decroly, B. Selisko, X. De Lamballerie, B. Coutard, B. Canard, M. Bolognesi
Recognition Of Rna Cap In The Wesselsbron Virus Ns5 Methyltransferase Domain: Implications For Rna-Capping Mechanisms In Flavivirus
J. Mol. Biol. V. 385 140 2009
PubMed-ID: 18976670 | Reference-DOI: 10.1016/J.JMB.2008.10.028

Molecule 1 - METHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.1.57
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST14
	Expression System Strain	:	C41 (DE3) PROS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NS5 N-TERMINAL METHYLTRANSFERASE DOMAIN, UNP RESIDUES 2500- 2791
	Organism Scientific	:	WESSELSBRON VIRUS
	Organism Taxid	:	164416
	Strain	:	SAH-177 99871-2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:56 , GLY A:81 , CYS A:82 , GLY A:83 , GLY A:86 , TRP A:87 , THR A:104 , LEU A:105 , HIS A:110 , SER A:130 , ASN A:131 , VAL A:132 , PHE A:133 , ASP A:146 , HOH A:4658 , HOH A:4676 , HOH A:4706 , HOH A:4793 , HOH A:4809	BINDING SITE FOR RESIDUE SAM A4633
2	AC2	SOFTWARE	ASN A:17 , MET A:18 , LEU A:19 , LYS A:95 , GLU A:169 , LYS A:172 , HIS A:173 , HOH A:4675	BINDING SITE FOR RESIDUE SO4 A4634
3	AC3	SOFTWARE	LYS A:21 , GLN A:22 , ARG A:170 , HOH A:4746	BINDING SITE FOR RESIDUE SO4 A4635
4	AC4	SOFTWARE	LYS A:21 , PHE A:24 , GLU A:169 , LYS A:194 , ARG A:197 , ARG A:201 , HOH A:4877	BINDING SITE FOR RESIDUE SO4 A4636
5	AC5	SOFTWARE	ARG A:37 , ARG A:41 , SER A:56 , ARG A:57 , ARG A:84 , HOH A:4861	BINDING SITE FOR RESIDUE SO4 A4637

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

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

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

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

(no "Exon" information available for 3ELU)

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:274
 aligned with C8XPB0_WSLV | C8XPB0 from UniProtKB/TrEMBL  Length:3405

    Alignment length:280
                                  2514      2524      2534      2544      2554      2564      2574      2584      2594      2604      2614      2624      2634      2644      2654      2664      2674      2684      2694      2704      2714      2724      2734      2744      2754      2764      2774      2784
         C8XPB0_WSLV   2505 VTLGEVWKRQLNMLGKQEFERYKVSDITEVDRTAARRYLKEGRTDVGISVSRGAAKIRWLHERGYLRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTLGIEGHEKPIHMQTLGWNIVKFKDKSNVFTMPTEPSDTLLCDIGESSSNPLVERDRTMKVLENFERWKHVNTENFCVKVLAPYHPDVIEKLERLQLRFGGGIVRVPFSRNSTHEMYYISGARNNITHMVNTTSRSLLRRMTRPSGKAIIEGDVFLPTGTRSVASEAGTIDHEALKLRVDQI 2784
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eluA01 A:6-258 Vaccinia Virus protein VP39                                                                                                                                                                                                                  --------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhh...eee.hhhhhhhhhhh..........hhhhhhhhhhhh.....eeeeee....hhhhhhhhh...eeeeeee................hhh.eeee..............eeee.......hhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eee............------.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3elu A    6 VTLGEVWKRQLNMLGKQEFERYKVSDITEVDRTAARRYLKEGRTDVGISVSRGAAKIRWLHERGYLRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTLGIEGHEKPIHMQTLGWNIVKFKDKSNVFTMPTEPSDTLLCDIGESSSNPLVERDRTMKVLENFERWKHVNTENFCVKVLAPYHPDVIEKLERLQLRFGGGIVRVPFSRNSTHEMYYISGARNNITHMVNTTSRSLLRRMTRPSGKAIIEGDVFLPTGTRSV------IDHEALKLRVDQI  285
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265|      275       285
                                                                                                                                                                                                                                                                                              266    273

Chain A from PDB  Type:PROTEIN  Length:274
 aligned with D0VX01_WSLV | D0VX01 from UniProtKB/TrEMBL  Length:275

    Alignment length:280
                                        1                                                                                                                                                                                                                                                                           
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
         D0VX01_WSLV      - ------------MLGKQEFERYKVSDITEVDRTAARRYLKEGRTDVGISVSRGAAKIRWLHERGYLRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTLGIEGHEKPIHMQTLGWNIVKFKDKSNVFTMPTEPSDTLLCDIGESSSNPLVERDRTMKVLENFERWKHVNTENFCVKVLAPYHPDVIEKLERLQLRFGGGIVRVPFSRNSTHEMYYISGARNNITHMVNTTSRSLLRRMTRPSGKAIIEGDVFLPTGTRSVASEAGTIDHEALKLRVDQI  268
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eluA01 A:6-258 Vaccinia Virus protein VP39                                                                                                                                                                                                                  --------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhh...eee.hhhhhhhhhhh..........hhhhhhhhhhhh.....eeeeee....hhhhhhhhh...eeeeeee................hhh.eeee..............eeee.......hhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eee............------.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3elu A    6 VTLGEVWKRQLNMLGKQEFERYKVSDITEVDRTAARRYLKEGRTDVGISVSRGAAKIRWLHERGYLRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTLGIEGHEKPIHMQTLGWNIVKFKDKSNVFTMPTEPSDTLLCDIGESSSNPLVERDRTMKVLENFERWKHVNTENFCVKVLAPYHPDVIEKLERLQLRFGGGIVRVPFSRNSTHEMYYISGARNNITHMVNTTSRSLLRRMTRPSGKAIIEGDVFLPTGTRSV------IDHEALKLRVDQI  285
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265|      275       285
                                                                                                                                                                                                                                                                                              266    273

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 3ELU)

Asymmetric/Biological 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)

Wesselsbron virus. Organism_taxid: 164416. Strain: sah-177 99871-2. (6)

3eluA01

A:6-258

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (C8XPB0_WSLV | C8XPB0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008026	ATP-dependent helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016817	hydrolase activity, acting on acid anhydrides	Catalysis of the hydrolysis of any acid anhydride.
	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:0004483	mRNA (nucleoside-2'-O-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0017111	nucleoside-triphosphatase activity	Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0070008	serine-type exopeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	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:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0039520	induction by virus of host autophagy	Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
	GO:0080009	mRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain A (D0VX01_WSLV | D0VX01)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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:0004483	mRNA (nucleoside-2'-O-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine.
	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.
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:0080009	mRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	3elu
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	D0VX01_WSLV \| D0VX01
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	2.1.1.57
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UniProtKB/Swiss-Prot
	C8XPB0_WSLV \| C8XPB0	:	3eld 3elw 3ely 3emb 3emd
UniProtKB/TrEMBL
	D0VX01_WSLV \| D0VX01	:	3eld 3elw 3ely 3emb 3emd

3eld	THE SAME PROTEIN IN COMPLEX WITH SINEFUNGIN
3elw	THE SAME PROTEIN COMPLEXED WITH ADOMET AND GPPPG
3ely	THE SAME PROTEIN COMPLEXED WITH ADOHCY
3emb	THE SAME PROTEIN COMPLEXED WITH ADOMET AND 7MEGPPPG
3emd	THE SAME PROTEIN COMPLEXED WITH SINEFUNGIN AND 7MEGPPPA

Description

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Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

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CATH Domains (1, 1)

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Gene Ontology (48, 58)

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