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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE VACCINIA POLYADENYLATE POLYMERASE HETERODIMER (APO FORM)

Authors :   C. M. Moure, B. R. Bowman, P. D. Gershon, F. A. Quiocho

Date :   08 Mar 06 (Deposition) - 16 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,D

Keywords :   Polyadenylate Polymerase, Pox Virus, Nucleotidyltransferase, Heterodimer, Processivity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Moure, B. R. Bowman, P. D. Gershon, F. A. Quiocho
Crystal Structures Of The Vaccinia Virus Polyadenylate Polymerase Heterodimer: Insights Into Atp Selectivity And Processivity.
Mol. Cell V. 22 339 2006
PubMed-ID: 16678106 | Reference-DOI: 10.1016/J.MOLCEL.2006.03.015
(for further references see the PDB file header)

Molecule 1 - CAP-SPECIFIC MRNA (NUCLEOSIDE-2'-O-)- METHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.1.57
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector	:	PPG177
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	VACCINIA VIRUS
	Organism Taxid	:	10245
	Synonym	:	POLYA, POLYMERASE REGULATORY SUBUNIT, POLYA, POLYMERASE SMALL SUBUNIT, PAP-S, VP39

Molecule 2 - POLY(A) POLYMERASE CATALYTIC SUBUNIT
	Chains	:	D
	EC Number	:	2.7.7.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 ROSETTA
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	VACCINIA VIRUS
	Organism Taxid	:	10245
	Synonym	:	POLYA, POLYMERASE LARGE SUBUNIT, PAP-L, VP55

		1	2
Asymmetric/Biological Unit	:	A	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2GAF)

(no "SS Bond" information available for 2GAF)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 2GAF)

Asymmetric/Biological 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

(no "Exon" information available for 2GAF)

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:286
 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 d2gafa_ A: automated match     es                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -2gafA00 A:2-297 Vaccinia      Virus protein VP39                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........-----....hhhhhhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhh....eeeeeee....hhhhh....eeeee...hhhhhhhhhhhhh...eeeee....------.hhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhh...eeee..eee...........eeeeee.......eeeehhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_MT_2O_PK  PDB: A:4-262 UniProt: 4-262                                                                                                                                                                                                                          ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gaf A   1 mDVVSLDKPFmYFEEIDNELDYEPES-----KKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWmLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVAS------PSTADLLSNYALQNVmISILNPVASSLKWRCPFPDQWIKDFYIPHGNKmLQPFAPSYSAEmRLLSIYTGENmRLTRVTKSDAVNYEKKmYYLNKIVRNKVVVNFDYPNQEYDYFHmYFmLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
                            |       10|       20     |   - |      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       
                            |        11-MSE         26    32                                                          92-MSE                                          141    148            163-MSE                          196-MSE     208-MSE    219-MSE          236-MSE                    263-MSE                              
                            1-MSE                                                                                                                                                                                                                                                                  266-MSE

Chain A from PDB  Type:PROTEIN  Length:286
 aligned with Q1PIV4_9POXV | Q1PIV4 from UniProtKB/TrEMBL  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       
         Q1PIV4_9POXV     1 MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSKRGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKLDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
               SCOP domains d2gafa_ A: automated match     es                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -2gafA00 A:2-297 Vaccinia      Virus protein VP39                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........-----....hhhhhhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhh....eeeeeee....hhhhh....eeeee...hhhhhhhhhhhhh...eeeee....------.hhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhh...eeee..eee...........eeeeee.......eeeehhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gaf A   1 mDVVSLDKPFmYFEEIDNELDYEPES-----KKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWmLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVAS------PSTADLLSNYALQNVmISILNPVASSLKWRCPFPDQWIKDFYIPHGNKmLQPFAPSYSAEmRLLSIYTGENmRLTRVTKSDAVNYEKKmYYLNKIVRNKVVVNFDYPNQEYDYFHmYFmLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
                            |       10|       20     |   - |      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       
                            1-MSE    11-MSE         26    32                                                          92-MSE                                          141    148            163-MSE                          196-MSE     208-MSE    219-MSE          236-MSE                    263-MSE                              
                                                                                                                                                                                                                                                                                                   266-MSE

Chain D from PDB  Type:PROTEIN  Length:447
 aligned with PAP1_VACCW | P23371 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:468
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
           PAP1_VACCW    12 NITLKIIETYLGRVPSVNEYHMLKLQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTIKAPNVISSKISYNVTSMEELARDMLNSMNVAVIDKAKVMGRHNVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF 479
               SCOP domains d2gafd_ D: Poly(A) polymerase catalytic subunit, PAPL                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........-----------..hhhhhhhhhhhhh....----------...hhhhhhhhhhhhhhhh...eeeehhhhhhh..........eeee.hhhhhhhhhhhhhhhhh...eeeee......eeeeee....eeeeeee.hhhhhhhh.eeee..eeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eee.....eeeee........eeeee.hhhhhhhhhhhh.....ee.hhhh..eeee....eeee.....ee......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..........ee..........eeee....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gaf D  12 NITLKIIETYLGRVPSVNEYHMLKSQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTIKAP-----------TSMEELARDMLNSMNVAVI----------VSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF 479
                                    21        31        41        51        61        71        81        91       101       111        |-         -|      141        |-       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
                                                                                                                                      120         132               150        161

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(

)

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)

Vaccinia virus. Organism_taxid: 10245. (9)

2gafA00

A:2-297

(no "Pfam Domain" information available for 2GAF)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q1PIV4_9POXV | Q1PIV4)

molecular function
	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:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.

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.

Chain D (PAP1_VACCW | P23371)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0004652	polynucleotide adenylyltransferase activity	Catalysis of the template-independent extension of the 3'- end of an RNA or DNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group.
	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: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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:70 - Pro A:71	[ RasMol ]
		His A:129 - Pro A:130	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 10)

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