1P39 - JenaLib

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Title :   DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG

Authors :   A. E. Hodel, P. D. Gershon, F. A. Quiocho

Date :   16 Dec 96 (Deposition) - 17 Sep 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Methyltransferase, Rna Cap, Poly(A) Polymerase, Vaccinia, Mrna Processing, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. E. Hodel, P. D. Gershon, X. Shi, S. M. Wang, F. A. Quiocho
Specific Protein Recognition Of An Mrna Cap Through Its Alkylated Base.
Nat. Struct. Biol. V. 4 350 1997
PubMed-ID: 9145102 | Reference-DOI: 10.1038/NSB0597-350
(for further references see the PDB file header)

Molecule 1 - VP39
	Cell Line	:	BL21
	Chains	:	A
	EC Number	:	2.7.7.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	BL21
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Mutation	:	YES
	Organism Scientific	:	VACCINIA VIRUS
	Organism Taxid	:	10254
	Strain	:	WR
	Synonym	:	POLY(A) POLYMERASE REGULATORY SUBUNIT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MGT	1	Ligand/Ion	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	MGT	2	Ligand/Ion	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:39 , LEU A:42 , TYR A:66 , GLY A:68 , SER A:69 , ALA A:70 , PRO A:71 , GLY A:72 , HIS A:74 , ILE A:94 , ASP A:95 , ARG A:97 , PHE A:115 , VAL A:116 , ASP A:138 , VAL A:139 , ARG A:140	BINDING SITE FOR RESIDUE SAH A 400
2	AC2	SOFTWARE	TYR A:22 , ARG A:177 , PHE A:180 , ASP A:182 , PRO A:202 , TYR A:204 , SER A:205 , GLU A:207 , GLU A:233 , HOH A:592 , HOH A:603 , HOH A:624 , HOH A:901	BINDING SITE FOR RESIDUE MGT A 401

(no "SS Bond" information available for 1P39)

Asymmetric Unit

No.	Residues
1	Ala A:70	-	Pro A:71
2	His A:129	-	Pro A:130

(no "SAP(SNP)/Variant" information available for 1P39)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_2O_PK	PS51612	Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile.	MCE_VACCW	4-262	1	A:4-262

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_2O_PK	PS51612	Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile.	MCE_VACCW	4-262	2	A:4-262

(no "Exon" information available for 1P39)

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
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Chain A from PDB  Type:PROTEIN  Length:291
 aligned with MCE_VACCW | P07617 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
            MCE_VACCW     1 MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSKRGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
               SCOP domains d1p39a_ A: Polymerase regulatory subunit VP39                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1p39A00 A:1-297 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh........hhhhh........hhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhh.....eeeeee.....hhh.....eeeee....hhhhhhhhhhh....eeeee....------..hhhhhhhhhhhhhhhhhh...eeeeee....hhh....eeee..eee...........eeeeee.......eeee.hhhhhhhhhhhhhhhh.hhh............hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_MT_2O_PK  PDB: A:4-262 UniProt: 4-262                                                                                                                                                                                                                          ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p39 A   1 MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRS------PSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
                                                                                                                                                                      141    148

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Polymerase regulatory subunit VP39 (19)

Vaccinia virus [TaxId: 10245] (17)

d1p39a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Vaccinia virus wr. Organism_taxid: 10254. Strain: wr. Cell_line: bl21. (5)

1p39A00

A:1-297

(no "Pfam Domain" information available for 1P39)

Asymmetric Unit(hide GO term definitions)

Chain A (MCE_VACCW | P07617)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
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: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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0031440	regulation of mRNA 3'-end processing	Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

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		Ala A:70 - Pro A:71	[ RasMol ]
		His A:129 - Pro A:130	[ RasMol ]

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	1p39
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