Structure of PDB 4by1 Chain A

Receptor sequence

>4by1A (length=1427) Species: 4932 (Saccharomyces cerevisiae)

VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKDEPELRVLSTEEILN
IFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGE
DDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIA
GQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNL
ELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDS
GDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHR
VKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPL
QIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGV
IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID
GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLH
NGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMT
LRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIA
QMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT
PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNS
LGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLD
PSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN
IRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQN
AQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVH
PGEMVGVLAAQSIGEPATQMTLNTVTSGVPRLKEILNVAKNMKTPSLTVY
LEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEI
IQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQT
FKNDLFVIWSEDNDEKLIIRCRVVRAEEDHMLKKIENTMLENITLRGVEN
IERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIY
TNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQ
GGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENV
ILGQMAPIGTGAFDVMIDEESLVKYMP

3D structure

• PDB: 4by1 Structures of RNA Polymerase II Complexes with Bye1, a Chromatin-Binding Phf3/Dido1 Homologue
• Chain: A
• Resolution: 3.6 Å

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	K101 A1108	K100 A1089
BS02	rna	A	I250 S251 D483 D485	I241 S242 D474 D476
BS03	dna	A	F252 K332 R344 R350 Q447 P448 T831 A832 E1403	F243 K323 R335 R341 Q438 P439 T822 A823 E1375
BS04	ZN	A	C107 C110 C148	C106 C109 C147
BS05	ZN	A	C70 C77 H80	C69 C76 H79
BS06	MG	A	D481 D483 D485	D472 D474 D476
BS07	APC	A	R446 P448 D481	R437 P439 D472

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

External links

• PDB: RCSB:4by1, PDBe:4by1, PDBj:4by1
• PDBsum: 4by1
• PubMed: 24003114
• UniProt: P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)