Structure of PDB 2vum Chain A

Receptor sequence

>2vumA (length=1418) 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
PGEMVGVLAAQSIGEPATQMTLNTFHVTSGVPRLKEILNVAKNMKTPSLT
VYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDE
EIIQLHFSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVI
WSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIERVVMMKY
DRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIME
VLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRH
GFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIG
TGAFDVMIDEESLVKYMP

3D structure

• PDB: 2vum Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation.
• Chain: A
• Resolution: 3.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D481 D483 D485 H1085
• Catalytic site (residue number reindexed from 1): D472 D474 D476 H1076
• 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	peptide	A	R726 A759 Q760 G766 Q767 Q768 S769 G772 G819 G820 E822 H1085	R717 A750 Q751 G757 Q758 Q759 S760 G763 G810 G811 E813 H1076
BS02	dna	A	K101 H1387	K100 H1350
BS03	rna	A	F252 K323 D485	F243 K314 D476
BS04	dna	A	K330 K332 R337 R350 Q447 A832 R1386	K321 K323 R328 R341 Q438 A823 R1349
BS05	ZN	A	C107 C110 C148	C106 C109 C147
BS06	ZN	A	C77 H80	C76 H79
BS07	MG	A	D481 D483 D485	D472 D474 D476

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:2vum, PDBe:2vum, PDBj:2vum
• PDBsum: 2vum
• PubMed: 18552824
• UniProt: P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)