Structure of PDB 1y77 Chain A

Receptor sequence
>1y77A (length=1416) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKDEPELRVLSTEEILN
IFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGE
DDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIA
GQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNL
ELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDS
GDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHR
VKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPL
QIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGV
IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID
GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLH
NGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMT
LRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIA
QMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT
PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNS
LGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLD
PSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN
IRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQN
AQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVH
PGEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVY
LEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEI
IQLHFSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWS
EDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDR
KVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVL
GIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGF
NRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTG
AFDVMIDEESLVKYMP
3D structure
PDB1y77 Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS
ChainA
Resolution4.5 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) D472 D474 D476
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 S318 R320 K330 K332 R350 Q447 T831 A832 G835 Y836 R1386 E1403 E1407 S309 R311 K321 K323 R341 Q438 T822 A823 G826 Y827 R1347 E1364 E1368
BS02 rna A F252 R320 R446 D485 F243 R311 R437 D476
BS03 ZN A C67 C70 H80 C66 C69 H79
BS04 MG A D481 D483 D485 D472 D474 D476
BS05 G2P A P448 N479 P439 N470
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:1y77, PDBe:1y77, PDBj:1y77
PDBsum1y77
PubMed15610738
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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