Structure of PDB 2nvx Chain A

Receptor sequence
>2nvxA (length=1402) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHI
SVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTF
KLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQA
LQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQV
GVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRID
LRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIP
YSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSP
QSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPA
IIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIF
GVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFST
GIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESF
EDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSAC
VGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFF
FHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVI
QFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLE
SGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRII
QNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDA
VTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMV
GVLAAQSIGEPATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGH
AADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHF
SLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDE
KLIIRCRVVRAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPS
PTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEA
GRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSN
TGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDV
MI
3D structure
PDB2nvx Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
ChainA
Resolution3.6 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D467 D469 D471
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 rna A S251 K323 D485 S237 K309 D471
BS02 dna A N1110 H1387 N1086 H1344
BS03 dna A K317 S318 R344 R350 Q447 T831 A832 G835 R839 R1386 E1403 K303 S304 R330 R336 Q433 T817 A818 G821 R825 R1343 E1360
BS04 ZN A C70 C77 H80 C68 C75 H78
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2nvx, PDBe:2nvx, PDBj:2nvx
PDBsum2nvx
PubMed17129781
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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