1F5A - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE

Authors :   G. Martin, W. Keller, S. Doublie

Date :   13 Jun 00 (Deposition) - 13 Sep 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Mrna Processing, Transferase, Transcription, Rna-Binding, Phosphorylation, Nuclear Protein, Alternative Splicing Helical Turn Motif, Nucleotidyl Transferase Catalytic Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Martin, W. Keller, S. Doublie
Crystal Structure Of Mammalian Poly(A) Polymerase In Complex With An Analog Of Atp.
Embo J. V. 19 4193 2000
PubMed-ID: 10944102 | Reference-DOI: 10.1093/EMBOJ/19.16.4193
(for further references see the PDB file header)

Molecule 1 - POLY(A) POLYMERASE
	Chains	:	A
	EC Number	:	2.7.7.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	C-TERMINAL DELETION MUTANT MISSING RESIDUES 514- 738
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 13)

No.	Name	Count	Type	Full Name
1	3AT	1	Ligand/Ion	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
2	3PO	1	Ligand/Ion	TRIPHOSPHATE
3	MN	3	Ligand/Ion	MANGANESE (II) ION
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:113 , ASP A:115 , ASP A:167 , 3AT A:1000 , MN A:1002 , HOH A:2155 , 3PO A:4000	BINDING SITE FOR RESIDUE MN A 1001
2	AC2	SOFTWARE	ASP A:113 , ASP A:115 , 3AT A:1000 , MN A:1001 , MN A:1003 , HOH A:2104 , 3PO A:4000	BINDING SITE FOR RESIDUE MN A 1002
3	AC3	SOFTWARE	3AT A:1000 , MN A:1002 , 3PO A:4000	BINDING SITE FOR RESIDUE MN A 1003
4	AC4	SOFTWARE	PHE A:100 , GLY A:101 , SER A:102 , THR A:109 , ASP A:115 , VAL A:154 , LYS A:158 , ASP A:167 , LYS A:228 , TYR A:237 , GLY A:246 , VAL A:247 , MN A:1001 , MN A:1002 , MN A:1003 , HOH A:2010 , HOH A:2045 , HOH A:2104 , HOH A:2127 , HOH A:2129 , HOH A:2155 , HOH A:2167 , 3PO A:4000	BINDING SITE FOR RESIDUE 3AT A 1000
5	AC5	SOFTWARE	ALA A:112 , ASP A:113 , 3AT A:1000 , MN A:1001 , MN A:1002 , MN A:1003 , HOH A:2155	BINDING SITE FOR RESIDUE 3PO A 4000

(no "SS Bond" information available for 1F5A)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:281	-	Pro A:282
2	Tyr A:320	-	Pro A:321

(no "SAP(SNP)/Variant" information available for 1F5A)

(no "PROSITE Motif" information available for 1F5A)

Asymmetric/Biological Unit (15, 15)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENSBTAT00000005300	1b	ENSBTAE00000429997	chr21:61558615-61558668	54	PAPOA_BOVIN	1-3	3	0	-	-
1.2	ENSBTAT00000005300	2	ENSBTAE00000392174	chr21:61572974-61573147	174	PAPOA_BOVIN	3-61	59	1	A:20-61	42
1.3	ENSBTAT00000005300	3	ENSBTAE00000042583	chr21:61573550-61573616	67	PAPOA_BOVIN	61-83	23	1	A:61-83	23
1.4	ENSBTAT00000005300	4	ENSBTAE00000042584	chr21:61576385-61576466	82	PAPOA_BOVIN	84-111	28	1	A:84-111	28
1.5	ENSBTAT00000005300	5	ENSBTAE00000042586	chr21:61578210-61578319	110	PAPOA_BOVIN	111-147	37	1	A:111-147	37
1.6	ENSBTAT00000005300	6	ENSBTAE00000042587	chr21:61578770-61578823	54	PAPOA_BOVIN	148-165	18	1	A:148-165	18
1.7	ENSBTAT00000005300	7	ENSBTAE00000042589	chr21:61581599-61581710	112	PAPOA_BOVIN	166-203	38	1	A:166-203	38
1.8	ENSBTAT00000005300	8	ENSBTAE00000042592	chr21:61582361-61582450	90	PAPOA_BOVIN	203-233	31	1	A:203-233	31
1.9	ENSBTAT00000005300	9	ENSBTAE00000042594	chr21:61582541-61582679	139	PAPOA_BOVIN	233-279	47	1	A:233-279	47
1.10	ENSBTAT00000005300	10	ENSBTAE00000381557	chr21:61584527-61584599	73	PAPOA_BOVIN	279-303	25	1	A:279-303	25
1.11	ENSBTAT00000005300	11	ENSBTAE00000042601	chr21:61585936-61586056	121	PAPOA_BOVIN	304-344	41	1	A:304-344	41
1.12	ENSBTAT00000005300	12	ENSBTAE00000042603	chr21:61587008-61587092	85	PAPOA_BOVIN	344-372	29	1	A:344-372	29
1.13	ENSBTAT00000005300	13	ENSBTAE00000042606	chr21:61591631-61591684	54	PAPOA_BOVIN	372-390	19	1	A:372-390	19
1.14	ENSBTAT00000005300	14	ENSBTAE00000042609	chr21:61592212-61592331	120	PAPOA_BOVIN	390-430	41	1	A:390-430 (gaps)	41
1.15	ENSBTAT00000005300	15	ENSBTAE00000042612	chr21:61593451-61593560	110	PAPOA_BOVIN	430-467	38	1	A:430-467 (gaps)	38
1.16	ENSBTAT00000005300	16	ENSBTAE00000042616	chr21:61595973-61596094	122	PAPOA_BOVIN	467-507	41	1	A:467-498	32
1.17	ENSBTAT00000005300	17	ENSBTAE00000042620	chr21:61599064-61599206	143	PAPOA_BOVIN	508-555	48	0	-	-
1.18	ENSBTAT00000005300	18	ENSBTAE00000246874	chr21:61601533-61601633	101	PAPOA_BOVIN	555-589	35	0	-	-
1.19	ENSBTAT00000005300	19	ENSBTAE00000042630	chr21:61601831-61602051	221	PAPOA_BOVIN	589-662	74	0	-	-
1.20	ENSBTAT00000005300	20	ENSBTAE00000042634	chr21:61605738-61605800	63	PAPOA_BOVIN	663-683	21	0	-	-
1.21	ENSBTAT00000005300	21	ENSBTAE00000042636	chr21:61607657-61607731	75	PAPOA_BOVIN	684-708	25	0	-	-
1.22a	ENSBTAT00000005300	22a	ENSBTAE00000378893	chr21:61609752-61610065	314	PAPOA_BOVIN	709-739	31	0	-	-

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:463
 aligned with PAPOA_BOVIN | P25500 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:479
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489         
          PAPOA_BOVIN    20 YGITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQLHQLLP 498
               SCOP domains d1f5aa4 A:20-214 Poly(A) polymerase, PAP, N-terminal domain                                                                                                                                        d1f5aa3 A:215-364 Poly(A) polymerase, PAP, middle domain                                                                                              d1f5aa1 A:365-498 Poly(A) polymerase, PAP, C-terminal domai      n                                                                     SCOP domains
               CATH domains 1f5aA03 A:20-52,A:209-365        1f5aA02 A:53-208 Beta Polymerase, domain 2                                                                                                                  1f5aA03 A:20-52,A:209-365  [code=1.10.1410.10, no name defined]                                                                                              1f5aA01 A:366-488  [code=3.30.70.590, no name defined]                                                                     ---------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....eeeehhhhhhh.......eeeeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee..eeeeeeeee.............hhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........................hhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....ee.------....eeeeeeeeee.----------.hhhhhhhhhhhhhhhhhhh.......eeeeeeee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:20-61 UniProt: 3-61      ----------------------Exon 1.4  PDB: A:84-111     ------------------------------------Exon 1.6          Exon 1.7  PDB: A:166-203              ---------------------------------------------------------------------------Exon 1.10  PDB: A:279-303Exon 1.11  PDB: A:304-344                ---------------------------Exon 1.13          ---------------------------------------Exon 1.15  PDB: A:430-467 (gaps)      ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3  PDB: A:61-83 ---------------------------Exon 1.5  PDB: A:111-147             -------------------------------------------------------Exon 1.8  PDB: A:203-233       --------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:344-372    -----------------Exon 1.14  PDB: A:390-430 (gaps)         ------------------------------------Exon 1.16  PDB: A:467-498        Transcript 1 (2)
           Transcript 1 (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:233-279 UniProt: 233-279      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1f5a A  20 YGITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAmLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLmPIITPAYPQQNSTYNVSVSTRmVmVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA------KEEFRTmWVIGLVFK----------DLTYDIQSFTDTVYRQAINSKmFEVDmKIAAmHVKRKQLHQLLP 498
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 |     259       269       279       289       299       309   |   319       329     | 339       349       359       369       379       389       399       409       419   |     -|     |439    |    -     | 459       469      |479 |    |489         
                                                                                                                                                                                                                                                                 251-MSE                                                       313-MSE               335-MSE                                                                                 423    430     |     444        455                  476-MSE|    |            
                                                                                                                                                                                                                                                                                                                                                       337-MSE                                                                                            436-MSE                                      481-MSE|            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            486-MSE

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: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.590, no name defined] (8)

Cattle (Bos taurus) (3)

1f5aA01

A:366-488

Topology: Beta Polymerase; domain 2 (187)

Homologous Superfamily: Beta Polymerase, domain 2 (183)

Cattle (Bos taurus) (3)

1f5aA02

A:53-208

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Poly(a)-polymerase, middle domain (9)

Homologous Superfamily: [code=1.10.1410.10, no name defined] (8)

Cattle (Bos taurus) (3)

1f5aA03

A:20-52,A:209-365

(no "Pfam Domain" information available for 1F5A)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PAPOA_BOVIN | P25500)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0031123	RNA 3'-end processing	Any process involved in forming the mature 3' end of an RNA molecule.
	GO:0043631	RNA polyadenylation	The enzymatic addition of a sequence of adenylyl residues at the 3' end of an RNA molecule.
	GO:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Trp A:281 - Pro A:282	[ RasMol ]
		Tyr A:320 - Pro A:321	[ RasMol ]

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	1f5a
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	PAPOA_BOVIN \| P25500	:	1q78 1q79

(no "Related Entries Specified in the PDB File" available for 1F5A)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (15, 15)

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