Structure of PDB 3gtj Chain A

Receptor sequence
>3gtjA (length=1429) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSEQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEE
ILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQ
RGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDN
DIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGD
PNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVI
RDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMM
AHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCA
VPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDW
DGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGML
IIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFW
LLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKH
GMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFI
NIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLR
GLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTT
RNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDH
TLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPL
PVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEI
IQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRS
VVHPGEMVGVLAAQSIGEPATQMTLNTFHVASKKVTSGVPRLKEILNVAK
NMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPR
STVIPEDEEIIQLHFSLLDEQQSPWLLRLELDRAAMNDKDLTMGQVGERI
KQTFKNDLFVIWSEDNDEKLIIRCRVVRPKEAEEDHMLKKIENTMLENIT
LRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGI
DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLV
DVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCR
GVSENVILGQMAPIGTGAFDVMIDEESLV
3D structure
PDB3gtj Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
ChainA
Resolution3.42 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 H1085
Catalytic site (residue number reindexed from 1) D475 D477 D479 H1079
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 L824 T827 D477 D479 L818 T821
BS02 dna A Q256 K332 R337 R344 R350 A832 Y836 Q250 K326 R331 R338 R344 A826 Y830
BS03 ZN A C107 C148 C167 C105 C146 C161
BS04 ZN A C70 C77 H80 C68 C75 H78
BS05 MG A D481 D483 D485 D475 D477 D479
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:3gtj, PDBe:3gtj, PDBj:3gtj
PDBsum3gtj
PubMed19478184
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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