Structure of PDB 6h68 Chain B

Receptor sequence

>6h68B (length=1175) Species: 559292 (Saccharomyces cerevisiae S288C)

ARTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGL
LNLGVKDIGEKVIFDGKPLNSNSGYLGNKLSVSVEQVSIAKPMSNDGVSS
AVERKVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVML
QSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPM
AIIRPSFANRGASYSHYGIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWR
KNEYLVPVVMILKALCHTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKK
RYPHLQNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKD
GSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKE
KIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFL
STGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTT
TVRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSIL
YSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEG
KTPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKEDIVG
PFEQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRN
MYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNF
PNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNG
DPITQHFGFGNDEWPKEWLEKLDEDGLPYIGTYVEEGDPICAYFDDTLNK
TKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDKFS
SRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLA
GKAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGAT
GEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGG
IRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVP
RIGSISTVCCRRCSMRFEDAKKLFIDDSQIWEDGQGNKFVGGNETTTVAI
PFVLKYLDSELSAMGIRLRYNVEPK

3D structure

• PDB: 6h68 Structural basis of RNA polymerase I stalling at UV light-induced DNA damage.
• Chain: B
• Resolution: 4.6 Å

Enzymatic activity

• 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	B	S482 R495 K924 H1038 R1065	S467 R480 K906 H1020 R1047
BS02	dna	B	I199 M430 S466 K513 N739 K740 Q1045 R1063 K1064 R1070	I184 M415 S451 K498 N724 K725 Q1027 R1045 K1046 R1052
BS03	dna	B	R219 P220 S221 R444 R448 M451 F508 L512	R204 P205 S206 R429 R433 M436 F493 L497
BS04	ZN	B	C1104 C1107 C1128 C1131	C1086 C1089 C1110 C1113

Gene Ontology

Molecular Function

• GO:0001054 RNA polymerase I activity
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006360 transcription by RNA polymerase I
• GO:0006361 transcription initiation at RNA polymerase I promoter
• GO:0006362 transcription elongation by RNA polymerase I
• GO:0006363 termination of RNA polymerase I transcription
• GO:0042254 ribosome biogenesis
• GO:0042790 nucleolar large rRNA transcription by RNA polymerase I

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005736 RNA polymerase I complex

External links

• PDB: RCSB:6h68, PDBe:6h68, PDBj:6h68
• PDBsum: 6h68
• PubMed: 30127008
• UniProt: P22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 (Gene Name=RPA135)