Structure of PDB 4y7n Chain A

Receptor sequence
>4y7nA (length=1393) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCDVPS
LVSRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTSL
GFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKA
NISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPV
KSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAK
TLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAG
DIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNL
SVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG
IVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLW
SGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTV
GSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIAD
GPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFL
NEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEG
KRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGRE
GLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDG
MDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGD
LKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFH
IDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLL
RSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSI
GEPATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAK
LIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWL
LRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRV
VAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEP
EWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEV
YNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSF
EETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI
3D structure
PDB4y7n Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
ChainA
Resolution3.3 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) D459 D461 D463
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 F252 K332 R344 R350 Q447 F230 K310 R322 R328 Q425
BS02 rna A R446 D485 R424 D463
BS03 ZN A C110 C167 C108 C157
BS04 ZN A C67 Q68 C77 H80 C65 Q66 C75 H78
BS05 MG A D481 D483 D485 D459 D461 D463
BS06 G2P A R446 P448 N479 T831 R424 P426 N457 T809
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:4y7n, PDBe:4y7n, PDBj:4y7n
PDBsum4y7n
PubMed26123024
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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