Structure of PDB 6upz Chain A

Receptor sequence
>6upzA (length=1382) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTSLGF
NEVFSRPEWMILTCLPVPPPPVRPSRGEDDLTFKLADILKANISLETLEH
NGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKG
KEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVT
PYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWK
VERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD
FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGI
RKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVA
IPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIH
VVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITE
TIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGR
LAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVD
RTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKT
AETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ
SLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDE
EYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDL
TIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRV
LQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL
KKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHT
TLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWLLRLELDRAA
MNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVDHMLKKIE
NTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLS
EVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVN
YRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGA
SAELDDCRGVSENVILGQMAPIGTGAFDVMID
3D structure
PDB6upz RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
ChainA
Resolution3.1 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 rna A D483 D485 D452 D454
BS02 dna A A309 R326 K332 R344 Q447 A832 G835 E1407 A278 R295 K301 R313 Q416 A801 G804 E1343
BS03 dna A K101 W139 K1109 H1387 K99 W137 K1068 H1323
BS04 ZN A C107 C167 C105 C155
BS05 ZN A C77 H80 C75 H78
BS06 MG A D481 D483 D485 D450 D452 D454
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6upz, PDBe:6upz, PDBj:6upz
PDBsum6upz
PubMed32284409
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

[Back to BioLiP]