DB code: S00412

RLCP classification	3.707.20000.110 : Transfer
CATH domain	3.40.50.150 : Rossmann fold	Catalytic domain
E.C.	2.1.1.57
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.40.50.150 : Rossmann fold	S00637 S00639 S00262 S00261 S00291 D00075 D00076 D00079 D00080 D00082 D00083 D00823

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P07617	Cap-specific mRNA (nucleoside-2''-O-)-methyltransferase	EC 2.1.1.57 Poly(A) polymerase regulatory subunit Poly(A) polymerase small subunit PAP-S VP39	YP_232977.1 (Protein) NC_006998.1 (DNA/RNA sequence)	PF01358 (PARP_regulatory) [Graphical View]

KEGG enzyme name
mRNA (nucleoside-2'-O-)-methyltransferase messenger ribonucleate nucleoside 2'-methyltransferase messenger RNA (nucleoside-2'-)-methyltransferase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P07617	PAP2_VACCV	S-adenosyl-L-methionine + m(7)G(5'')pppR-RNA = S-adenosyl-L-homocysteine + m(7)G(5'')pppRm-RNA.	Methyltransferase activity: Monomer, poly(A) polymerase activity: Heterodimer of VP55 (catalytic) and VP39 (regulatory).

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates		Products		Intermediates
KEGG-id	C00019	C02339	C00021	C04802
E.C.
Compound	S-adenosyl-L-methionine	m7G(5')pppR-RNA	S-adenosyl-L-homocysteine	m7G(5')pppRm-RNA (mRNA containing a 2'-O-methylpurine cap)
Type	amino acids,amine group,nucleoside,sulfonium ion	nucleic acids,nucleotide	amino acids,amine group,nucleoside,sulfide group	nucleic acids,nucleotide
ChEBI	67040 67040		16680 57856 16680 57856
PubChem	34755 34755		25246222 439155 25246222 439155

1av6A	Unbound	Analogue:MGT-__G-__A-__A-__A-__A-__A (chain B)	Bound:SAH	Unbound
1b42A	Unbound	Unbound	Bound:SAH	Unbound
1bkyA	Unbound	Unbound	Bound:SAH	Unbound
1eamA	Unbound	Unbound	Bound:SAH	Unbound
1eqaA	Unbound	Analogue:MG7	Bound:SAH	Unbound
1jszA	Unbound	Unbound	Bound:SAH	Unbound
1jteA	Unbound	Unbound	Bound:SAH	Unbound
1jtfA	Unbound	Analogue:M7G	Bound:SAH	Unbound
1p39A	Unbound	Analogue:MGT	Bound:SAH	Unbound
1v39A	Unbound	Analogue:M7G	Bound:SAH	Unbound
1vp3A	Unbound	Unbound	Bound:SAH	Unbound
1vp9A	Unbound	Unbound	Bound:SAH	Unbound
1vptA	Bound:SAM	Unbound	Unbound	Unbound
2vp3A	Unbound	Analogue:M7G	Bound:SAH	Unbound
3magA	Unbound	Unbound	Bound:SAH	Unbound
3mctA	Unbound	Unbound	Bound:SAH	Unbound
4dcgA	Unbound	Analogue:MG7	Bound:SAH	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [8]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1av6A	LYS 41;LYS 175
1b42A	LYS 41;LYS 175
1bkyA	LYS 41;LYS 175
1eamA	LYS 41;LYS 175				mutant E233A
1eqaA	LYS 41;LYS 175				mutant E233Q
1jszA	LYS 41;LYS 175
1jteA	LYS 41;LYS 175				mutant F180W
1jtfA	LYS 41;LYS 175				mutant F180W
1p39A	LYS 41;LYS 175
1v39A	LYS 41;LYS 175
1vp3A	LYS 41;LYS 175
1vp9A	LYS 41;LYS 175
1vptA	LYS 41;LYS 175				mutant R140A, K142A, R143A
2vp3A	LYS 41;LYS 175
3magA	LYS 41;LYS 175
3mctA	LYS 41;LYS 175
4dcgA	LYS 41;LYS 175				mutant D182A

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[8]	p.446

References
[1]
Resource
Comments
Medline ID
PubMed ID	1670500
Journal	Cell
Year	1991
Volume	66
Pages	1269-78
Authors	Gershon PD, Ahn BY, Garfield M, Moss B
Title	Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus.
Related PDB
Related UniProtKB	P07617
[2]
Resource
Comments
Medline ID
PubMed ID	1313572
Journal	Proc Natl Acad Sci U S A
Year	1992
Volume	89
Pages	2897-901
Authors	Schnierle BS, Gershon PD, Moss B
Title	Cap-specific mRNA (nucleoside-O2'-)-methyltransferase and poly(A) polymerase stimulatory activities of vaccinia virus are mediated by a single protein.
Related PDB
Related UniProtKB	P07617
[3]
Resource
Comments
Medline ID
PubMed ID	8846300
Journal	RNA
Year	1996
Volume	2
Pages	88-101
Authors	Shi X, Yao P, Jose T, Gershon P
Title	Methyltransferase-specific domains within VP-39, a bifunctional protein that participates in the modification of both mRNA ends.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	8612277
Journal	Cell
Year	1996
Volume	85
Pages	247-56
Authors	Hodel AE, Gershon PD, Shi X, Quiocho FA
Title	The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.
Related PDB	1vpt
Related UniProtKB	P07617
[5]
Resource
Comments
Medline ID
PubMed ID	9118948
Journal	EMBO J
Year	1997
Volume	16
Pages	1103-13
Authors	Deng L, Gershon PD
Title	Interplay of two uridylate-specific RNA binding sites in the translocation of poly(A) polymerase from vaccinia virus.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	9145102
Journal	Nat Struct Biol
Year	1997
Volume	4
Pages	350-4
Authors	Hodel AE, Gershon PD, Shi X, Wang SM, Quiocho FA
Title	Specific protein recognition of an mRNA cap through its alkylated base.
Related PDB	1p39 1v39 1vp3 1vp9 2vp3
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	9287339
Journal	J Biol Chem
Year	1997
Volume	272
Pages	23292-302
Authors	Shi X, Bernhardt TG, Wang SM, Gershon PD
Title	The surface region of the bifunctional vaccinia RNA modifying protein VP39 that interfaces with Poly(A) polymerase is remote from the RNA binding cleft used for its mRNA 5' cap methylation function.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	9660928
Journal	Mol Cell
Year	1998
Volume	1
Pages	443-7
Authors	Hodel AE, Gershon PD, Quiocho FA
Title	Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme.
Related PDB	1av6
Related UniProtKB	P07617
[9]
Resource
Comments
Medline ID
PubMed ID	9622508
Journal	Biochemistry
Year	1998
Volume	37
Pages	8564-74
Authors	Lockless SW, Cheng HT, Hodel AE, Quiocho FA, Gershon PD
Title	Recognition of capped RNA substrates by VP39, the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID	9657944
Journal	Virology
Year	1998
Volume	246
Pages	253-65
Authors	Gershon PD, Shi X, Hodel AE
Title	Evidence that the RNA methylation and poly(A) polymerase stimulatory activities of vaccinia virus protein VP39 do not impinge upon one another.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	9917386
Journal	J Mol Biol
Year	1999
Volume	285
Pages	1417-27
Authors	Deng L, Johnson L, Neveu JM, Hardin S, Wang SM, Lane WS, Gershon PD
Title	A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5' end-binding "cleft".
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID	10377383
Journal	Proc Natl Acad Sci U S A
Year	1999
Volume	96
Pages	7149-54
Authors	Hu G, Gershon PD, Hodel AE, Quiocho FA
Title	mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.
Related PDB	1b42 1bky 1eam 1eqa 3mag 3mct 4dcg
Related UniProtKB
[13]
Resource
Comments	Review
Medline ID
PubMed ID	10766517
Journal	Curr Opin Struct Biol
Year	2000
Volume	10
Pages	75-7
Authors	Rhodes D, Burley SK
Title	Protein-nucleic acid interactions.
Related PDB
Related UniProtKB
[14]
Resource
Comments	Review
Medline ID
PubMed ID	10679461
Journal	Curr Opin Struct Biol
Year	2000
Volume	10
Pages	78-86
Authors	Quiocho FA, Hu G, Gershon PD
Title	Structural basis of mRNA cap recognition by proteins.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID	11076512
Journal	Biochemistry
Year	2000
Volume	39
Pages	13730-6
Authors	Hsu PC, Hodel MR, Thomas JW, Taylor LJ, Hagedorn CH, Hodel AE
Title	Structural requirements for the specific recognition of an m7G mRNA cap.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID	12056899
Journal	Biochemistry
Year	2002
Volume	41
Pages	7677-87
Authors	Hu G, Oguro A, Li C, Gershon PD, Quiocho FA
Title	The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap.
Related PDB	1jsz 1jte 1jtf
Related UniProtKB

Comments
This enzyme is a bifunctional protein, which methylates the ribose 2' OH group of the first transcribed nucleotide, and also act as a regulatory subunit of poly(A) polymerase, VP55, which creates the 3' poly(A) tail of mRNA's. This protein binds to poly(A), as a regulatory subunit. According to the literature [8], the active site of this enzyme is similar to that of COMT (S00291 in EzCatDB), although it does not utilize a cofactor magnesium ion, unlike COMT. According to the literature [8], the reaction proceeds as follows: (1) The positively charged sidechains of Lys41 and Lys175 act as modulator, which activate the acceptor, the oxygen atom of the 2' OH group, by lowering the pKa of the acceptor group, together with the positively charged sulfur atom of another substrate, SAM. (2) The activated acceptor group makes a nucleophilic attack on the transferred group, the methyl group of SAM. (Probably, the reaction proceeds through an SN2-like mechanism, leading to the inversion of configuration of the methyl group, as in COMT.)

Comments

This enzyme is a bifunctional protein, which methylates the ribose 2' OH group of the first transcribed nucleotide, and also act as a regulatory subunit of poly(A) polymerase, VP55, which creates the 3' poly(A) tail of mRNA's. This protein binds to poly(A), as a regulatory subunit.
According to the literature [8], the active site of this enzyme is similar to that of COMT (S00291 in EzCatDB), although it does not utilize a cofactor magnesium ion, unlike COMT. According to the literature [8], the reaction proceeds as follows:
(1) The positively charged sidechains of Lys41 and Lys175 act as modulator, which activate the acceptor, the oxygen atom of the 2' OH group, by lowering the pKa of the acceptor group, together with the positively charged sulfur atom of another substrate, SAM.
(2) The activated acceptor group makes a nucleophilic attack on the transferred group, the methyl group of SAM. (Probably, the reaction proceeds through an SN2-like mechanism, leading to the inversion of configuration of the methyl group, as in COMT.)

Created	Updated
2002-08-30	2009-02-26