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Protein

Virion DNA-directed RNA polymerase

Gene
N/A
Organism
Enterobacteria phage N4 (Bacteriophage N4)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase, which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure.2 Publications

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).1 Publication

Cofactori

Mg2+1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1556 – 15561Magnesium2 Publications
Metal bindingi1948 – 19481Magnesium2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1434 – 14374ATP2 Publications
Nucleotide bindingi1556 – 15616ATP2 Publications
Nucleotide bindingi1667 – 16682ATP2 Publications

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. GTP binding Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

ATP-binding, GTP-binding, Manganese, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Virion DNA-directed RNA polymeraseImported (EC:2.7.7.61 Publication)
Short name:
vRNAP
OrganismiEnterobacteria phage N4 (Bacteriophage N4)Imported
Taxonomic identifieri10752 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaeN4likevirus
Virus hostiEscherichia coli [TaxID: 562]
ProteomesiUP000001789: Genome

Subcellular locationi

Virion 1 Publication

Keywords - Cellular componenti

DNA-directed RNA polymerase, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 35003500Virion DNA-directed RNA polymerasePRO_0000431828Add
BLAST

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PO4X-ray2.00A998-2101[»]
3C2PX-ray2.00A/B998-2102[»]
3C3LX-ray2.40A/B998-2102[»]
3C46X-ray2.00A/B998-2102[»]
3Q0AX-ray2.69A/B998-2103[»]
3Q22X-ray2.11A/B998-2103[»]
3Q23X-ray1.80A/B998-2103[»]
3Q24X-ray1.81A/B998-2102[»]
4FF1X-ray2.47A/B998-2103[»]
4FF2X-ray2.00A/B998-2103[»]
4FF3X-ray2.00A/B998-2103[»]
4FF4X-ray2.03A/B998-2103[»]
ProteinModelPortaliQ859P9.
SMRiQ859P9. Positions 1008-2101.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ859P9.

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili2078 – 211134Sequence AnalysisAdd
BLAST
Coiled coili2777 – 281034Sequence AnalysisAdd
BLAST

Domaini

Contains three functional domains; the central domain possesses the transcriptional activity.1 Publication

Sequence similaritiesi

Keywords - Domaini

Coiled coil

Sequencei

Sequence statusi: Complete.

Q859P9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSVFDRLAGF ADSVTNAKQV DVSTATAQKK AEQGVTTPLV SPDAAYQMQA
60 70 80 90 100
ARTGNVGANA FEPGTVQSDF MNLTPMQIMN KYGVEQGLQL INARADAGNQ
110 120 130 140 150
VFNDSVTTRT PGEELGDIAT GVGLGFVNTL GGIGALGAGL LNDDAGAVVA
160 170 180 190 200
QQLSKFNDAV HATQSQALQD KRKLFAARNL MNEVESERQY QTDKKEGTND
210 220 230 240 250
IVASLSKFGR DFVGSIENAA QTDSIISDGL AEGVGSLLGA GPVLRGASLL
260 270 280 290 300
GKAVVPANTL RSAALAGAID AGTGTQSLAR IASTVGRAAP GMVGVGAMEA
310 320 330 340 350
GGAYQQTADE IMKMSLKDLE KSPVYQQHIK DGMSPEQARR QTASETGLTA
360 370 380 390 400
AAIQLPIAAA TGPLVSRFEM APFRAGSLGA VGMNLARETV EEGVQGATGQ
410 420 430 440 450
LAQNIAQQQN IDKNQDLLKG VGTQAGLGAL YGFGSAGVVQ APAGAARLAG
460 470 480 490 500
AATAPVLRTT MAGVKAAGSV AGKVVSPIKN TLVARGERVM KQNEEASPVA
510 520 530 540 550
DDYVAQAAQE AMAQAPEAEV TIRDAVEATD ATPEQKVAAH QYVSDLMNAT
560 570 580 590 600
RFNPENYQEA PEHIRNAVAG STDQVQVIQK LADLVNTLDE SNPQALMEAA
610 620 630 640 650
SYMYDAVSEF EQFINRDPAA LDSIPKDSPA IELLNRYTNL TANIQNTPKV
660 670 680 690 700
IGALNVINRM INESAQNGSL NVTEESSPQE MQNVALAAEV APEKLNPESV
710 720 730 740 750
NVVLKHAADG RIKLNNRQIA ALQNAAAILK GAREYDAEAA RLGLRPQDIV
760 770 780 790 800
SKQIKTDESR TQEGQYSALQ HANRIRSAYN SGNFELASAY LNDFMQFAQH
810 820 830 840 850
MQNKVGALNE HLVTGNADKN KSVHYQALTA DREWVRSRTG LGVNPYDTKS
860 870 880 890 900
VKFAQQVALE AKTVADIANA LASAYPELKV SHIKVTPLDS RLNAPAAEVV
910 920 930 940 950
KAFRQGNRDV ASSQPKADSV NQVKETPVTK QEPVTSTVQT KTPVSESVKT
960 970 980 990 1000
EPTTKESSPQ AIKEPVNQSE KQDVNLTNED NIKQPTESVK ETETSTKEST
1010 1020 1030 1040 1050
VTEELKEGID AVYPSLVGTA DSKAEGIKNY FKLSFTLPEE QKSRTVGSEA
1060 1070 1080 1090 1100
PLKDVAQALS SRARYELFTE KETANPAFNG EVIKRYKELM EHGEGIADIL
1110 1120 1130 1140 1150
RSRLAKFLNT KDVGKRFAQG TEANRWVGGK LLNIVEQDGD TFKYNEQLLQ
1160 1170 1180 1190 1200
TAVLAGLQWR LTATSNTAIK DAKDVAAITG IDQALLPEGL VEQFDTGMTL
1210 1220 1230 1240 1250
TEAVSSLAQK IESYWGLSRN PNAPLGYTKG IPTAMAAEIL AAFVESTDVV
1260 1270 1280 1290 1300
ENIVDMSEID PDNKKTIGLY TITELDSFDP INSFPTAIEE AVLVNPTEKM
1310 1320 1330 1340 1350
FFGDDIPPVA NTQLRNPAVR NTPEQKAALK AEQATEFYVH TPMVQFYETL
1360 1370 1380 1390 1400
GKDRILELMG AGTLNKELLN DNHAKSLEGK NRSVEDSYNQ LFSVIEQVRA
1410 1420 1430 1440 1450
QSEDISTVPI HYAYNMTRVG RMQMLGKYNP QSAKLVREAI LPTKATLDLS
1460 1470 1480 1490 1500
NQNNEDFSAF QLGLAQALDI KVHTMTREVM SDELTKLLEG NLKPAIDMMV
1510 1520 1530 1540 1550
EFNTTGSLPE NAVDVLNTAL GDRKSFVALM ALMEYSRYLV AEDKSAFVTP
1560 1570 1580 1590 1600
LYVEADGVTN GPINAMMLMT GGLFTPDWIR NIAKGGLFIG SPNKTMNEHR
1610 1620 1630 1640 1650
STADNNDLYQ ASTNALMESL GKLRSNYASN MPIQSQIDSL LSLMDLFLPD
1660 1670 1680 1690 1700
INLGENGALE LKRGIAKNPL TITIYGSGAR GIAGKLVSSV TDAIYERMSD
1710 1720 1730 1740 1750
VLKARAKDPN ISAAMAMFGK QAASEAHAEE LLARFLKDME TLTSTVPVKR
1760 1770 1780 1790 1800
KGVLELQSTG TGAKGKINPK TYTIKGEQLK ALQENMLHFF VEPLRNGITQ
1810 1820 1830 1840 1850
TVGESLVYST EQLQKATQIQ SVVLEDMFKQ RVQEKLAEKA KDPTWKKGDF
1860 1870 1880 1890 1900
LTQKELNDIQ ASLNNLAPMI ETGSQTFYIA GSENAEVANQ VLATNLDDRM
1910 1920 1930 1940 1950
RVPMSIYAPA QAGVAGIPFM TIGTGDGMMM QTLSTMKGAP KNTLKIFDGM
1960 1970 1980 1990 2000
NIGLNDITDA SRKANEAVYT SWQGNPIKNV YESYAKFMKN VDFSKLSPEA
2010 2020 2030 2040 2050
LEAIGKSALE YDQRENATVD DIANAASLIE RNLRNIALGV DIRHKVLDKV
2060 2070 2080 2090 2100
NLSIDQMAAV GAPYQNNGKI DLSNMTPEQQ ADELNKLFRE ELEARKQKVA
2110 2120 2130 2140 2150
KARAEVKEET VSEKEPVNPD FGMVGREHKA SGVRILSATA IRNLAKISNL
2160 2170 2180 2190 2200
PSTQAATLAE IQKSLAAKDY KIIYGTPTQV AEYARQKNVT ELTSQEMEEA
2210 2220 2230 2240 2250
QAGNIYGWTN FDDKTIYLVS PSMETLIHEL VHASTFEEVY SFYQGNEVSP
2260 2270 2280 2290 2300
TSKQAIENLE GLMEQFRSLD ISKDSPEMRE AYADAIATIE GHLSNGFVDP
2310 2320 2330 2340 2350
AISKAAALNE FMAWGLANRA LAAKQKRTSS LVQMVKDVYQ AIKKLIWGRK
2360 2370 2380 2390 2400
QAPALGEDMF SNLLFNSAIL MRSQPTTQAV AKDGTLFHSK AYGNNERLSQ
2410 2420 2430 2440 2450
LNQTFDKLVT DYLRTDPVTE VERRGNVANA LMSATRLVRD VQSHGFNMTA
2460 2470 2480 2490 2500
QEQSVFQMVT AALATEAAID PHAMARAQEL YTHVMKHLTV EHFMADPDST
2510 2520 2530 2540 2550
NPADRYYAQQ KYDTISGANL VEVDAKGRTS LLPTFLGLAM VNEELRSIIK
2560 2570 2580 2590 2600
EMPVPKADKK LGNDIDTLLT NAGTQVMESL NRRMAGDQKA TNVQDSIDAL
2610 2620 2630 2640 2650
SETIMAAALK RESFYDAVAT PTGNFIDRAN QYVTDSIERL SETVIEKADK
2660 2670 2680 2690 2700
VIANPSNIAA KGVAHLAKLT AAIASEKQGE IVAQGVMTAM NQGKVWQPFH
2710 2720 2730 2740 2750
DLVNDIVGRT KTNANVYDLI KLVKSQISQD RQQFREHLPT VIAGKFSRKL
2760 2770 2780 2790 2800
TDTEWSAMHT GLGKTDLAVL RETMSMAEIR DLLSSSKKVK DEISTLEKEI
2810 2820 2830 2840 2850
QNQAGRNWNL VQKKSKQLAQ YMIMGEVGNN LLRNAHAISR LLGERITNGP
2860 2870 2880 2890 2900
VADVAAIDKL ITLYSLELMN KSDRDLLSEL AQSEVEGMEF SIAYMVGQRT
2910 2920 2930 2940 2950
EEMRKAKGDN RTLLNHFKGY IPVENQQGVN LIIADDKEFA KLNSQSFTRI
2960 2970 2980 2990 3000
GTYQGSTGFR TGSKGYYFSP VAARAPYSQG ILQNVRNTAG GVDIGTGFTL
3010 3020 3030 3040 3050
GTMVAGRITD KPTVERITKA LAKGERGREP LMPIYNSKGQ VVAYEQSVDP
3060 3070 3080 3090 3100
NMLKHLNQDN HFAKMVGVWR GRQVEEAKAQ RFNDILIEQL HAMYEKDIKD
3110 3120 3130 3140 3150
SSANKSQYVN LLGKIDDPVL ADAINLMNIE TRHKAEELFG KDELWVRRDM
3160 3170 3180 3190 3200
LNDALGYRAA SIGDVWTGNS RWSPSTLDTV KKMFLGAFGN KAYHVVMNAE
3210 3220 3230 3240 3250
NTIQNLVKDA KTVIVVKSVV VPAVNFLANI YQMIGRGVPV KDIAVNIPRK
3260 3270 3280 3290 3300
TSEINQYIKS RLRQIDAEAE LRAAEGNPNL VRKLKTEIQS ITDSHRRMSI
3310 3320 3330 3340 3350
WPLIEAGEFS SIADAGISRD DLLVAEGKIH EYMEKLANKL PEKVRNAGRY
3360 3370 3380 3390 3400
ALIAKDTALF QGIQKTVEYS DFIAKAIIYD DLVKRKKKSS SEALGQVTEE
3410 3420 3430 3440 3450
FINYDRLPGR FRGYMESMGL MWFYNFKIRS IKVAMSMIRN NPVHSLIATV
3460 3470 3480 3490 3500
VPAPTMFGNV GLPIQDNMLT MLAEGRLDYS LGFGQGLRAP TLNPWFNLTH
Length:3,500
Mass (Da):382,495
Last modified:December 12, 2006 - v2
Checksum:iB4A52EAC2E28BBDB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF056009 Genomic DNA. Translation: AAO24831.2.
RefSeqiYP_950528.1. NC_008720.1.

Genome annotation databases

GeneIDi5075715.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF056009 Genomic DNA. Translation: AAO24831.2.
RefSeqiYP_950528.1. NC_008720.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PO4X-ray2.00A998-2101[»]
3C2PX-ray2.00A/B998-2102[»]
3C3LX-ray2.40A/B998-2102[»]
3C46X-ray2.00A/B998-2102[»]
3Q0AX-ray2.69A/B998-2103[»]
3Q22X-ray2.11A/B998-2103[»]
3Q23X-ray1.80A/B998-2103[»]
3Q24X-ray1.81A/B998-2102[»]
4FF1X-ray2.47A/B998-2103[»]
4FF2X-ray2.00A/B998-2103[»]
4FF3X-ray2.00A/B998-2103[»]
4FF4X-ray2.03A/B998-2103[»]
ProteinModelPortaliQ859P9.
SMRiQ859P9. Positions 1008-2101.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi5075715.

Miscellaneous databases

EvolutionaryTraceiQ859P9.

Family and domain databases

ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence and analysis of bacteriophage N4."
    Hendrix R.W., Rothman-Denes L., Hatfull G.F., Lawrence J.G., Pedulla M.
    Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "Virion-associated RNA polymerase required for bacteriophage N4 development."
    Falco S.C., Laan K.V., Rothman-Denes L.B.
    Proc. Natl. Acad. Sci. U.S.A. 74:520-523(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  3. "Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase."
    Gleghorn M.L., Davydova E.K., Rothman-Denes L.B., Murakami K.S.
    Mol. Cell 32:707-717(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 998-2102, FUNCTION.
  4. "X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase."
    Murakami K.S., Davydova E.K., Rothman-Denes L.B.
    Proc. Natl. Acad. Sci. U.S.A. 105:5046-5051(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 998-2101, FUNCTION.
  5. "X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides."
    Gleghorn M.L., Davydova E.K., Basu R., Rothman-Denes L.B., Murakami K.S.
    Proc. Natl. Acad. Sci. U.S.A. 108:3566-3571(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 998-2103 IN COMPLEX WITH ATP AND MANGANESE, COFACTOR.
  6. "Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography."
    Basu R.S., Murakami K.S.
    J. Biol. Chem. 288:3305-3311(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 998-2103 IN COMPLEX WITH ATP AND MANGANESE, COFACTOR.

Entry informationi

Entry nameiRPOLV_BPN4
AccessioniPrimary (citable) accession number: Q859P9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 4, 2015
Last sequence update: December 12, 2006
Last modified: February 4, 2015
This is version 57 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.