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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DENGUE-2 VIRUS METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE

Authors :   A. A. Thompson, B. J. Geiss, O. B. Peersen

Date :   13 Oct 08 (Deposition) - 06 Jan 09 (Release) - 03 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Dengue Virus, Flavivirus, Ns5 Methyltransferase, Rna Cap Binding, Atp-Binding, Capsid Protein, Cleavage On Pair Of Basic Residues, Endoplasmic Reticulum, Envelope Protein, Glycoprotein, Helicase, Hydrolase, Membrane, Metal-Binding, Multifunctional Enzyme, Nucleotide-Binding, Nucleotidyltransferase, Nucleus, Phosphoprotein, Protease, Ribonucleoprotein, Rna Replication, Rna-Binding, Rna- Directed Rna Polymerase, Secreted, Serine Protease, Transcription, Transcription Regulation, Transmembrane, Viral Nucleoprotein, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. J. Geiss, A. A. Thompson, A. J. Andrews, R. L. Sons, H. H. Gari, S. M. Keenan, O. B. Peersen
Analysis Of Flavivirus Ns5 Methyltransferase Cap Binding.
J. Mol. Biol. V. 385 1643 2009
PubMed-ID: 19101564 | Reference-DOI: 10.1016/J.JMB.2008.11.058
(for further references see the PDB file header)

Molecule 1 - RNA-DIRECTED RNA POLYMERASE NS5
	Chains	:	A
	EC Number	:	2.1.1.56, 2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKKT7E
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN 1-267 OF RNA-DIRECTED RNA
	Organism Scientific	:	DENGUE VIRUS 2 16681-PDK53
	Organism Taxid	:	31635
	Polymerase Ns5	:	UNP RESIDUES 2493-2757
	Strain	:	16681

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:38 , LYS A:42 , SER A:56 , ARG A:57 , ARG A:84 , HOH A:536	BINDING SITE FOR RESIDUE SO4 A 902
2	AC2	SOFTWARE	LYS A:105 , HIS A:110 , SER A:150 , SER A:151 , ARG A:160 , HOH A:504 , HOH A:517	BINDING SITE FOR RESIDUE SO4 A 903
3	AC3	SOFTWARE	GLY A:109 , HIS A:110 , GLU A:111 , SAH A:901	BINDING SITE FOR RESIDUE SO4 A 904
4	AC4	SOFTWARE	ASP A:131 , VAL A:156 , ARG A:160 , SAH A:901	BINDING SITE FOR RESIDUE SO4 A 905
5	AC5	SOFTWARE	LYS A:30 , ARG A:212	BINDING SITE FOR RESIDUE SO4 A 906
6	AC6	SOFTWARE	SER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:86 , TRP A:87 , THR A:104 , LYS A:105 , VAL A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , ILE A:147 , HOH A:516 , HOH A:546 , SO4 A:904 , SO4 A:905	BINDING SITE FOR RESIDUE SAH A 901

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

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

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

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

(no "Exon" information available for 3EVG)

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
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Chain A from PDB  Type:PROTEIN  Length:257
 aligned with POLG_DEN27 | P29991 from UniProtKB/Swiss-Prot  Length:3391

    Alignment length:257
                                  2508      2518      2528      2538      2548      2558      2568      2578      2588      2598      2608      2618      2628      2638      2648      2658      2668      2678      2688      2698      2708      2718      2728      2738      2748       
          POLG_DEN27   2499 TLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNMVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFIPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRYKKATYEPDVDLGSGTRN 2755
               SCOP domains d3evga_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3evgA00 A:8-264 Vaccinia Virus protein VP39                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhh..eeeehhhhhhhhhh.........hhhhhhhhhhh.......eeeeee....hhhhhhhhh...eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhhhh.....eeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3evg A    8 TLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNMVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFIPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRYKKATYEPDVDLGSGTRN  264
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: mRNA cap methylase (41)

Protein domain: automated matches (8)

Dengue virus 2 16681-pdk53 [TaxId: 31635] (1)

d3evga_

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)

Dengue virus 2 16681-pdk53. Organism_taxid: 31635. Strain: 16681. (1)

3evgA00

A:8-264

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (POLG_DEN27 | P29991)

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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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: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: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: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: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:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	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: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: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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0039564	suppression by virus of host STAT2 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT2 (signal transducer and activator of transcription-2) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes.
	GO:0039574	suppression by virus of host TYK2 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host TYK2 (tyrosine kinase 2) activity. TYK2 is an intracellular signal-transducing tyrosine kinase that associates with the cytoplasmic tails of cytokine receptors and transmits the cytokine signal by phosphorylating receptor subunits.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0044165	host cell endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0044167	host cell endoplasmic reticulum membrane	The lipid bilayer surrounding the host cell endoplasmic reticulum.
	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:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. 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.

Asymmetric/Biological Unit
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3eva	CRYSTAL STRUCTURE OF YELLOW FEVER VIRUS METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE
3evb	CRYSTAL STRUCTURE OF YELLOW FEVER VIRUS METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE, CRYSTAL FORM II
3evc	CRYSTAL STRUCTURE OF GTP COMPLEX OF YELLOW FEVER VIRUS METHYLTRANSFERASE AND S-ADENOSYL-L-HOMOCYSTEINE
3evd	CRYSTAL STRUCTURE OF GTP COMPLEX OF YELLOW FEVER VIRUS METHYLTRANSFERASE AND S-ADENOSYL-L-HOMOCYSTEINE, CRYSTAL FORM II
3eve	CRYSTAL STRUCTURE OF GPPPA COMPLEX OF YELLOW FEVER VIRUS METHYLTRANSFERASE AND S-ADENOSYL-L-HOMOCYSTEINE
3evf	CRYSTAL STRUCTURE OF ME7-GPPPA COMPLEX OF YELLOW FEVER VIRUS METHYLTRANSFERASE AND S-ADENOSYL-L-HOMOCYSTEINE

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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SCOP Domains (1, 1)

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Gene Ontology (63, 63)

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