Structure of PDB 8k5p Chain A

Receptor sequence
>8k5pA (length=1408) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLN
DPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCE
CVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPS
EDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKPELRVLSTEEILNIFKH
ISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLT
FKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQ
ALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQ
VGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRI
DLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVI
PYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVS
PQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTP
AIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQII
FGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFS
TGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRES
FEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSA
CVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEF
FFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNV
IQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLL
ESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRI
IQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRD
AVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEM
VGVLAAQSIGEPATQMTLKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGH
AADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHF
DQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEK
LIIRCRVVRDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGE
YVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAA
LYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGAL
MRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDE
ESLVKYMP
3D structure
PDB8k5p Structural basis of exoribonuclease-mediated mRNA transcription termination
ChainA
Resolution2.8 Å
3D
structure
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Enzymatic activity
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 R175 K1109 H1387 R171 K1085 H1340
BS02 rna A R63 I250 S251 R446 D485 R59 I237 S238 R433 D472
BS03 dna A F252 K317 K332 R344 T831 A832 G835 R1386 E1403 F239 K304 K319 R331 T818 A819 G822 R1339 E1356
BS04 ZN A C107 C148 C167 C103 C144 C163
BS05 ZN A C67 C70 H80 C63 C66 H76
BS06 MG A D481 D483 D485 D468 D470 D472
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:8k5p, PDBe:8k5p, PDBj:8k5p
PDBsum8k5p
PubMed38538796
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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