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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF POLYMERASE DOMAIN OF THE BACTERIOPHAGE N4 VIRION RNA POLYMERASE
 
Authors :  K. S. Murakami, E. K. Davydova, L. B. Rothman-Denes
Date :  25 Apr 07  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Right Hand Shape, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Murakami, E. K. Davydova, L. B. Rothman-Denes
X-Ray Crystal Structure Of Polymerase Domain Of The Bacteriophage N4 Virion Rna Polymerase
Proc. Natl. Acad. Sci. Usa V. 15 5046 2008
PubMed-ID: 18362338  |  Reference-DOI: 10.1073/PNAS.0712325105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIRION RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PEKD27
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PBAC
    Fragment: RNA POLYMERASE
    Gene: GP50
    Organism Scientific: ENTEROBACTERIA PHAGE N4
    Organism Taxid: 10752

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PO4)

(-) Sites  (0, 0)

(no "Site" information available for 2PO4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PO4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PO4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PO4)

(-) Exons   (0, 0)

(no "Exon" information available for 2PO4)

(-) Sequences/Alignments

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:1094
 aligned with RPOLV_BPN4 | Q859P9 from UniProtKB/Swiss-Prot  Length:3500

    Alignment length:1094
                                  1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627      1637      1647      1657      1667      1677      1687      1697      1707      1717      1727      1737      1747      1757      1767      1777      1787      1797      1807      1817      1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937      1947      1957      1967      1977      1987      1997      2007      2017      2027      2037      2047      2057      2067      2077      2087      2097    
          RPOLV_BPN4   1008 GIDAVYPSLVGTADSKAEGIKNYFKLSFTLPEEQKSRTVGSEAPLKDVAQALSSRARYELFTEKETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGTEANRWVGGKLLNIVEQDGDTFKYNEQLLQTAVLAGLQWRLTATSNTAIKDAKDVAAITGIDQALLPEGLVEQFDTGMTLTEAVSSLAQKIESYWGLSRNPNAPLGYTKGIPTAMAAEILAAFVESTDVVENIVDMSEIDPDNKKTIGLYTITELDSFDPINSFPTAIEEAVLVNPTEKMFFGDDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGTLNKELLNDNHAKSLEGKNRSVEDSYNQLFSVIEQVRAQSEDISTVPIHYAYNMTRVGRMQMLGKYNPQSAKLVREAILPTKATLDLSNQNNEDFSAFQLGLAQALDIKVHTMTREVMSDELTKLLEGNLKPAIDMMVEFNTTGSLPENAVDVLNTALGDRKSFVALMALMEYSRYLVAEDKSAFVTPLYVEADGVTNGPINAMMLMTGGLFTPDWIRNIAKGGLFIGSPNKTMNEHRSTADNNDLYQASTNALMESLGKLRSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLVSSVTDAIYERMSDVLKARAKDPNISAAMAMFGKQAASEAHAEELLARFLKDMETLTSTVPVKRKGVLELQSTGTGAKGKINPKTYTIKGEQLKALQENMLHFFVEPLRNGITQTVGESLVYSTEQLQKATQIQSVVLEDMFKQRVQEKLAEKAKDPTWKKGDFLTQKELNDIQASLNNLAPMIETGSQTFYIAGSENAEVANQVLATNLDDRMRVPMSIYAPAQAGVAGIPFMTIGTGDGMMMQTLSTMKGAPKNTLKIFDGMNIGLNDITDASRKANEAVYTSWQGNPIKNVYESYAKFMKNVDFSKLSPEALEAIGKSALEYDQRENATVDDIANAASLIERNLRNIALGVDIRHKVLDKVNLSIDQMAAVGAPYQNNGKIDLSNMTPEQQADELNKLFREELEARKQKVAK 2101
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...............hhhhhhee.............hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.hhhhh..hhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeee............eeeeee......hhhhhh.hhhhhhhh.......ee.........ee..eeeee.hhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.ee..eee.....eee........hhhhhh.ee...eee......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhheee..eeeeee.hhhhhhhhhhhh....hhhhhhhhhh..eee.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...................hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh..ee....ee...eeee......eee........ee..eeee.....hhhhhhhhhhhhhhhhhhhhhh.......ee...eeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..ee.....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2po4 A   11 GIDAVYPSLVGTADSKAEGIKNYFKLSFTLPEEQKSRTVGSEAPLKDVAQALSSRARYELFTEKETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGTEANRWVGGKLLNIVEQDGDTFKYNEQLLQTAVLAGLQWRLTATSNTAIKDAKDVAAITGIDQALLPEGLVEQFDTGMTLTEAVSSLAQKIESYWGLSRNPNAPLGYTKGIPTAMAAEILAAFVESTDVVENIVDMSEIDPDNKKTIGLYTITELDSFDPINSFPTAIEEAVLVNPTEKMFFGDDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGTLNKELLNDNHAKSLEGKNRSVEDSYNQLFSVIEQVRAQSEDISTVPIHYAYNMTRVGRMQMLGKYNPQSAKLVREAILPTKATLDLSNQNNEDFSAFQLGLAQALDIKVHTMTREVMSDELTKLLEGNLKPAIDMMVEFNTTGSLPENAVDVLNTALGDRKSFVALMALMEYSRYLVAEDKSAFVTPLYVEADGVTNGPINAMMLMTGGLFTPDWIRNIAKGGLFIGSPNKTMNEHRSTADNNDLYQASTNALMESLGKLRSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLVSSVTDAIYERMSDVLKARAKDPNISAAMAMFGKQAASEAHAEELLARFLKDMETLTSTVPVKRKGVLELQSTGTGAKGKINPKTYTIKGEQLKALQENMLHFFVEPLRNGITQTVGESLVYSTEQLQKATQIQSVVLEDMFKQRVQEKLAEKAKDPTWKKGDFLTQKELNDIQASLNNLAPMIETGSQTFYIAGSENAEVANQVLATNLDDRMRVPMSIYAPAQAGVAGIPFMTIGTGDGMMMQTLSTMKGAPKNTLKIFDGMNIGLNDITDASRKANEAVYTSWQGNPIKNVYESYAKFMKNVDFSKLSPEALEAIGKSALEYDQRENATVDDIANAASLIERNLRNIALGVDIRHKVLDKVNLSIDQMAAVGAPYQNNGKIDLSNMTPEQQADELNKLFREELEARKQKVAK 1104
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2PO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PO4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PO4)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RPOLV_BPN4 | Q859P9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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: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:0032774    RNA biosynthetic process    The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  2po4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RPOLV_BPN4 | Q859P9: 3c2p 3c3l 3c46 3q0a 3q22 3q23 3q24 4ff1 4ff2 4ff3 4ff4

(-) Related Entries Specified in the PDB File

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