Structure of PDB 6bqf Chain A

Receptor sequence
>6bqfA (length=1372) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCGGCG
NTQPTIRKDGLKLVGSWVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEW
MILTCLPVPPPPVRPSIEDDLTFKLADILKANISLETLEHNGAPHHAIEE
AESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLM
GKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQL
VRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDP
VLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHV
PQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFI
ELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF
DEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQV
CAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVL
DVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLN
NVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDD
YSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL
VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDA
AFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRK
FLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVK
DLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA
FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTKVTSGVPRLKE
ILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIY
YDPDPRSTVIPEDEEIIQLHFSQQSPWLLRLELDRAAMNDKDLTMGQVGE
RIKQTFKNDLFVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLR
GVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP
TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV
MTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGV
SENVILGQMAPIGTGAFDVMID
3D structure
PDB6bqf Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
ChainA
Resolution3.35 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) D440 D442 D444
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 dna A K330 K332 R337 Q447 Y836 E1403 K289 K291 R296 Q406 Y795 E1329
BS02 ZN A C107 C110 C167 C105 C108 C149
BS03 ZN A C67 C77 H80 C65 C75 H78
BS04 MG A D481 D483 D485 D440 D442 D444
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:6bqf, PDBe:6bqf, PDBj:6bqf
PDBsum6bqf
PubMed29487211
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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