C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1426019545  54 QRATVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFKFSHN 100
Cdd:cd10507     1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1426019545  54 QRATVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFKFSHN 100
Cdd:cd10507     1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1426019545  41 ELVGVDEEKDNKRQraTVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFK 96
Cdd:COG1594    46 EIIVVEEEEVEGLP--TTKVICPKCGNDEAYWWLKQTRSADEPETRFFRCTKCGHT 99

transcription factor S, archaeal; This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. [Transcription, Transcription factors]

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1426019545  57 TVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKF 95
Cdd:TIGR01384  60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY 98

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1426019545  54 QRATVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFKFSHN 100
Cdd:cd10507     1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1426019545  54 QRATVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFKF 97
Cdd:cd00656     1 TLPTTDRTCPKCGHDEAYWWMLQTRSADEPPTRFYKCTKCGHTW 44

C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1426019545   61 ECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFKFS 98
Cdd:smart00440   2 ECPKCGNREATFYQLQTRSADEPMTVFYVCTKCGHHWR 39

C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1426019545  57 TVDEECPKCGNPEMEYYTLQLRSADEGQTVFYECPKCKFK 96
Cdd:cd10511     4 TTKITCPKCGHDEAYWWMVQTRSADEPPTRFYKCTKCGHT 43

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1426019545  62 CPKCGNPEMEYYTLQLRSADEGQTVFYECPKC--KFKF 97
Cdd:cd13749    10 CGKCKKRKCTYYQLQTRSADEPMTTFVTCLNCgnRWKF 47

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1426019545  52 KRQRATVDE-ECPKCGNPEMEYYTLQLRSADEGQTVFYECPKC--KFKFS 98
Cdd:TIGR01385 250 KIQKAVTDLfTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECgnRWKFC 299