2PI4 - JenaLib

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Title :   T7RNAP COMPLEXED WITH A PHI10 PROTEIN AND INITIATING GTPS.

Authors :   W. P. Kennedy, J. R. Momand, Y. W. Yin

Date :   12 Apr 07 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,P,T

Keywords :   T7 Rna Polymerase, Initiating Nucleotides. , Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. P. Kennedy, J. R. Momand, Y. W. Yin
Mechanism For De Novo Rna Synthesis And Initiating Nucleotide Specificity By T7 Rna Polymerase.
J. Mol. Biol. V. 370 256 2007
PubMed-ID: 17512007 | Reference-DOI: 10.1016/J.JMB.2007.03.041
(for further references see the PDB file header)

*Molecule 1 - 5'- D(CPTPTPCPCPTPAPTPAPGPTPGPAPGPTPCPGPTPAP TPTPA)-3'*
	Chains	:	T
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(TPAPAPTPAPCPGPAPCPTPCPAPCPT)- 3'*
	Chains	:	P
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DNA-DIRECTED RNA POLYMERASE
	Chains	:	A
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	1
	Organism Scientific	:	ENTEROBACTERIA PHAGE T7
	Organism Taxid	:	10760

		1	2	3
Asymmetric/Biological Unit	:	A	P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GH3	2	Ligand/Ion	3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GH3 A:901	BINDING SITE FOR RESIDUE MG A 884
2	AC2	SOFTWARE	ASP A:537 , ASP A:812 , GH3 A:902	BINDING SITE FOR RESIDUE MG A 885
3	AC3	SOFTWARE	ARG A:394 , ARG A:425 , ASN A:437 , ILE A:810 , MG A:884 , GH3 A:902 , DC T:5	BINDING SITE FOR RESIDUE GH3 A 901
4	AC4	SOFTWARE	TYR A:571 , ARG A:627 , TYR A:639 , HIS A:784 , ASP A:812 , MG A:885 , GH3 A:901 , DC T:4 , DC T:5	BINDING SITE FOR RESIDUE GH3 A 902

(no "SS Bond" information available for 2PI4)

(no "Cis Peptide Bond" information available for 2PI4)

(no "SAP(SNP)/Variant" information available for 2PI4)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNA_POL_PHAGE_1	PS00900	Bacteriophage-type RNA polymerase family active site signature 1.	RPOL_BPT7	533-544	1	A:533-544
2	RNA_POL_PHAGE_2	PS00489	Bacteriophage-type RNA polymerase family active site signature 2.	RPOL_BPT7	625-639	1	A:625-639

(no "Exon" information available for 2PI4)

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:862
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:878
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875        
            RPOL_BPT7     6 IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
               SCOP domains d2pi4a_ A: T7 RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --2pi4A01 A:8-325 T7 RNA polymerase, domain 1                                                                                                                                                                                                                                                                                   2pi4A02 A:326-411  [code=1.10.287.260, no name defined]                               ---------2pi4A03                      2pi4A04 A:450-527  [code=1.10.287.280, no name defined]                       2pi4A03                   2pi4A05 A:554-784 5' to 3' exonuclease, C-terminal subdomain                                                                                                                                                                           2pi4A03 A:421-449,A:528-553,A:785-872  [code=3.30.70.370, no name defined]              ----------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_pol-2pi4A01 A:449-883                                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhh..----------------.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................................hhhhhhhhhhhhhhhhhhhh..eeeeee........eeeeeehhhhhhhhhh........................................ee..hhhhhhhh....hhhhhhhhhhhhh.eeeehhhhhhhhhhhh..............................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..eeee....eee........hhhhhhhee....eehhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhh...ee...........hhhhhhhhh.hhhhhhhh.........hhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.................eee.....eee........ee...hhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pi4 A   6 IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMF----------------PLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
                                    15        25        35        45        55         -      | 75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875        
                                                                            55               72

Chain P from PDB  Type:DNA  Length:14
                                              
                 2pi4 P 101 TAATACGACTCACT 114
                                   110

Chain T from PDB  Type:DNA  Length:22
                                                      
                 2pi4 T   1 CTTCCTATAGTGAGTCGTATTA  22
                                    10        20

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: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: T7 RNA polymerase (12)

Protein domain: T7 RNA polymerase (11)

Bacteriophage T7 [TaxId: 10760] (11)

d2pi4a_

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RNA_pol] (7)

Family: RNA_pol (7)

Enterobacteria phage T7 (Bacteriophage T7) (7)

RNA_pol-2pi4A01

A:449-883

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RPOL_BPT7 | P00573)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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:0039695	DNA-templated viral transcription	A transcription process that uses a viral DNA as a template.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 2pi4)

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	2.7.7.6
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	RPOL_BPT7 \| P00573	:	1aro 1cez 1h38 1msw 1qln 1s0v 1s76 1s77 2pi5 3e2e 3e3j 4rnp

2pi5	T7 RNA POLYMERASE COMPLEXED WITH A PHI10 PROMOTER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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