Structure of PDB 3hoy Chain A

Receptor sequence
>3hoyA (length=1419) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDEPELRVLSTEEIL
NIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRG
EDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDI
AGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPN
LELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRD
SGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAH
RVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVP
LQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDG
VIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLII
DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLL
HNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGM
TLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINI
AQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGL
TPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRN
SLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTL
DPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPV
NIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQ
NAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVV
HPGEMVGVLAAQSIGEPATQMTLSKKVTSGVPRLKEILNVAKNMKTPSLT
VYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDE
EIIQLHFSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVI
WSEDNDEKLIIRCRVVRAEEDHMLKKIENTMLENITLRGVENIERVVMMK
YDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIM
EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR
HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPI
GTGAFDVMIDEESLVKYMP
3D structure
PDB3hoy Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
ChainA
Resolution3.4 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) D473 D475 D477
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 K332 R350 Q447 T831 A832 G835 Y836 R1386 E1403 S310 K324 R342 Q439 T823 A824 G827 Y828 R1350 E1367
BS02 dna A K101 W139 A1108 K100 W138 A1091
BS03 ZN A C107 C110 C148 C106 C109 C147
BS04 ZN A C70 C77 H80 C69 C76 H79
BS05 MG A D481 D483 D485 D473 D475 D477
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:3hoy, PDBe:3hoy, PDBj:3hoy
PDBsum3hoy
PubMed19560423
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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