Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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RPOLCX RNA polymerase subunit CX

SMART accession number:	SM00659
Description:	present in RNA polymerase I, II and III
Interpro abstract (IPR006591):	DNA-directed RNA polymerases EC 2.7.7.6 (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [ (PUBMED:3052291) ]. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [ (PUBMED:10499798) ]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits. This family includes the DNA-directed RNA polymerases I, II, and III subunit RPABC4 (also known as RPC10 and ABC10-alpha) [ (PUBMED:10559229) ] and archaeal polymerase subunit P [ (PUBMED:19419240) ].
GO process:	transcription, DNA-templated (GO:0006351)
GO function:	DNA binding (GO:0003677), DNA-directed 5'-3' RNA polymerase activity (GO:0003899)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 800 RPOLCX domains in 799 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing RPOLCX domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RPOLCX domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing RPOLCX domain in the selected taxonomic class.

• Cellular role (predicted cellular role)

• Cellular role: transcription
  

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Shpakovski GV, Acker J, Wintzerith M, Lacroix JF, Thuriaux P, Vigneron M
  • Four subunits that are shared by the three classes of RNA polymerase are functionally interchangeable between Homo sapiens and Saccharomyces cerevisiae.
  • Mol Cell Biol. 1995; 15: 4702-10
  • Display abstract

  • Four cDNAs encoding human polypeptides hRPB7.0, hRPB7.6, hRPB17, and hRPB14.4 (referred to as Hs10 alpha, Hs10 beta, Hs8, and Hs6, respectively), homologous to the ABC10 alpha, ABC10 beta, ABC14.5, and ABC23 RNA polymerase subunits (referred to as Sc10 alpha, Sc10 beta, Sc8, and Sc6, respectively) of Saccharomyces cerevisiae, were cloned and characterized for their ability to complement defective yeast mutants. Hs10 alpha and the corresponding Sp10 alpha of Schizosaccharomyces pombe can complement an S. cerevisiae mutant (rpc10-delta::HIS3) defective in Sc10 alpha. The peptide sequences are highly conserved in their carboxy-terminal halves, with an invariant motif CX2CX12RCX2CGXR corresponding to a canonical zinc-binding domain. Hs10 beta, Sc10 beta, and the N subunit of archaeal RNA polymerase are homologous. An invariant CX2CGXnCCR motif presumably forms an atypical zinc-binding domain. Hs10 beta, but not the archaeal subunit, complemented an S. cerevisiae mutant (rpb10-delta 1::HIS3) lacking Sc10 beta. Hs8 complemented a yeast mutant (rpb8-delta 1::LYS2) defective in the corresponding Sc8 subunit, although with a strong thermosensitive phenotype. Interspecific complementation also occurred with Hs6 and with the corresponding Dm6 cDNA of Drosophila melanogaster. Hs6 cDNA and the Sp6 cDNA of S. pombe are dosage-dependent suppressors of rpo21-4, a mutation generating a slowly growing yeast defective in the largest subunit of RNA polymerase II. Finally, a doubly chimeric S. cerevisiae strain bearing the Sp6 cDNA and the human Hs10 beta cDNA was also viable. No interspecific complementation was observed for the human hRPB25 (Hs5) homolog of the yeast ABC27 (Sc5) subunit.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• % proteins involved KEGG pathway ID Description 100.00 map03020 RNA polymerase This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with RPOLCX domain which could be assigned to a KEGG orthologous group, and not all proteins containing RPOLCX domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of RPOLCX domains in PDB

  PDB code	Main view	Title
  1i3q		RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION
  1i50		RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION
  1i6h		RNA POLYMERASE II ELONGATION COMPLEX
  1k83		Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin
  1nik		Wild Type RNA Polymerase II
  1nt9		Complete 12-subunit RNA polymerase II
  1pqv		RNA polymerase II-TFIIS complex
  1r5u		RNA POLYMERASE II TFIIB COMPLEX
  1r9s		RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE
  1r9t		RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE
  1sfo		RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX
  1twa		RNA polymerase II complexed with ATP
  1twc		RNA polymerase II complexed with GTP
  1twf		RNA polymerase II complexed with UTP at 2.3 A resolution
  1twg		RNA polymerase II complexed with CTP
  1twh		RNA polymerase II complexed with 2'dATP
  1wcm		Complete 12-Subunit RNA Polymerase II at 3.8 A
  1y1v		Refined RNA Polymerase II-TFIIS complex
  1y1w		Complete RNA Polymerase II elongation complex
  1y1y		RNA Polymerase II-TFIIS-DNA/RNA complex
  1y77		Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP
  2b63		Complete RNA Polymerase II-RNA inhibitor complex
  2b8k		12-subunit RNA Polymerase II
  2e2h		RNA polymerase II elongation complex at 5 mM Mg2+ with GTP
  2e2i		RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP
  2e2j		RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP
  2ja5		CPD lesion containing RNA Polymerase II elongation complex A
  2ja6		CPD lesion containing RNA Polymerase II elongation complex B
  2ja7		CPD lesion containing RNA Polymerase II elongation complex C
  2ja8		CPD lesion containing RNA Polymerase II elongation complex D
  2nvq		RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP
  2nvt		RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP
  2nvx		RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP
  2nvy		RNA Polymerase II form II in 150 mM Mn+2
  2nvz		RNA Polymerase II elongation complex with UTP, updated 11/2006
  2pmz		Archaeal RNA polymerase from Sulfolobus solfataricus
  2r7z		Cisplatin lesion containing RNA polymerase II elongation complex
  2r92		Elongation complex of RNA polymerase II with artificial RdRP scaffold
  2r93		Elongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop
  2vum		Alpha-amanitin inhibited complete RNA polymerase II elongation complex
  2waq		The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase
  2wb1		The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase
  2y0s		Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group
  2yu9		RNA polymerase II elongation complex in 150 mm MG+2 with UTP
  3cqz		Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin
  3fki		12-Subunit RNA Polymerase II Refined with Zn-SAD data
  3gtg		Backtracked RNA polymerase II complex with 12mer RNA
  3gtj		Backtracked RNA polymerase II complex with 13mer RNA
  3gtk		Backtracked RNA polymerase II complex with 18mer RNA
  3gtl		Backtracked RNA polymerase II complex with 13mer with G<>U mismatch
  3gtm		Co-complex of Backtracked RNA polymerase II with TFIIS
  3gto		Backtracked RNA polymerase II complex with 15mer RNA
  3gtp		Backtracked RNA polymerase II complex with 24mer RNA
  3gtq		Backtracked RNA polymerase II complex induced by damage
  3h0g		RNA Polymerase II from Schizosaccharomyces pombe
  3h3v		Yeast RNAP II containing poly(A)-signal sequence in the active site
  3hkz		The X-ray crystal structure of RNA polymerase from Archaea
  3hou		Complete RNA polymerase II elongation complex I with a T-U mismatch
  3hov		Complete RNA polymerase II elongation complex II
  3how		Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine
  3hox		Complete RNA polymerase II elongation complex V
  3hoy		Complete RNA polymerase II elongation complex VI
  3hoz		Complete RNA polymerase II elongation complex IV with a T-U mismatch and a frayed RNA 3'-guanine
  3i4m		8-oxoguanine containing RNA polymerase II elongation complex D
  3i4n		8-oxoguanine containing RNA polymerase II elongation complex E
  3j0k		Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly
  3j1n		Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module
  3k1f		Crystal structure of RNA Polymerase II in complex with TFIIB
  3k7a		Crystal Structure of an RNA polymerase II-TFIIB complex
  3m3y		RNA polymerase II elongation complex C
  3m4o		RNA polymerase II elongation complex B
  3po2		Arrested RNA Polymerase II elongation complex
  3po3		Arrested RNA Polymerase II reactivation intermediate
  3qt1		RNA polymerase II variant containing A Chimeric RPB9-C11 subunit
  3rzd		RNA Polymerase II Initiation Complex with a 5-nt RNA
  3rzo		RNA Polymerase II Initiation Complex with a 4-nt RNA
  3s14		RNA Polymerase II Initiation Complex with a 6-nt RNA
  3s15		RNA Polymerase II Initiation Complex with a 7-nt RNA
  3s16		RNA Polymerase II Initiation Complex with an 8-nt RNA
  3s17		RNA Polymerase II Initiation Complex with a 9-nt RNA
  3s1m		RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 1)
  3s1n		RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2)
  3s1q		RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with ATP
  3s1r		RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with GTP
  3s2d		RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U
  3s2h		RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP
  4a3b		RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid
  4a3c		RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid
  4a3d		RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid
  4a3e		RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP
  4a3f		RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid and soaked with AMPCPP
  4a3g		RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid
  4a3i		RNA Polymerase II binary complex with DNA
  4a3j		RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with GMPCPP
  4a3k		RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid
  4a3l		RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with AMPCPP
  4a3m		RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with AMPCPP
  4a93		RNA Polymerase II elongation complex containing a CPD Lesion
  4ayb		RNAP at 3.2Ang
  4bbr		Structure of RNA polymerase II-TFIIB complex
  4bbs		Structure of an initially transcribing RNA polymerase II-TFIIB complex
  4bxx		Structures of RNA polymerase II complexes with Bye1, a chromatin- binding PHF3 DIDO homologue
  4bxz		RNA Polymerase II-Bye1 complex
  4by1		elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP
  4by7		elongating RNA Polymerase II-Bye1 TLD complex
  4c2m		Structure of RNA polymerase I at 2.8 A resolution
  4c3h		Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93
  4c3i		Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100
  4c3j		Structure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90
  4qiw		4QIW
  4v1m		4V1M
  4v1n		4V1N
  4v1o		4V1O
  4v8s		4V8S
  4x67		4X67
  4x6a		4X6A
  4y52		4Y52
  4y7n		4Y7N
  4ym7		4YM7
  5c3e		5C3E
  5c44		5C44
  5c4a		5C4A
  5c4j		5C4J
  5c4x		5C4X
  5fj8		5FJ8
  5fj9		5FJ9
  5fja		5FJA
  5flm		5FLM
  5fmf		5FMF
  5fyw		5FYW
  5fz5		5FZ5
  5g5l		5G5L
  5ip7		5IP7
  5ip9		5IP9
  5iy6		5IY6
  5iy7		5IY7
  5iy8		5IY8
  5iy9		5IY9
  5iya		5IYA
  5iyb		5IYB
  5iyc		5IYC
  5iyd		5IYD
  5m3f		5M3F
  5m3m		5M3M
  5sva		5SVA

• Links (links to other resources describing this domain)

• INTERPRO	IPR006591

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