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 71649339  79 QGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEKED 125
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 71649339  79 QGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEKED 125
Cdd:cd10507   1 KGATIEEKCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFSEN 47

Transcription factor S-II (TFIIS);

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 71649339    86 RCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEK 123
Cdd:pfam01096   2 KCPKCGNREAYFFQLQTRSADEPMTVFYVCTKCGHRWR 39

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

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 71649339     87 CPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEKE 124
Cdd:smart00440   3 CPKCGNREATFYQLQTRSADEPMTVFYVCTKCGHHWRE 40

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 71649339  79 QGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEKED 125
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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71649339  19 FCSDCGSVLplpGAQDTV-TCIRCGFNINVRDFEGKVVKTSVvfHQLGTAMPMsVEEGPECQGPVVDRRCPRCGHEGMAY 97
Cdd:COG1594   2 FCPKCGSMM---KPKDGVlVCPKCGYEEPRDEEAEAKYVSTE--EQEDKEIIV-VEEEEVEGLPTTKVICPKCGNDEAYW 75

                        90       100
                ....*....|....*....|.
gi 71649339  98 HTRQMRSADEGQTVFYTCTNC 118
Cdd:COG1594  76 WLKQTRSADEPETRFFRCTKC 96

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        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71649339    19 FCSDCGSV-LPLPGaqdTVTCIRCGFNINVRDFEGKVVKTSVVFHQLGTAMpmsVEEGPECQGPVVDRRCPRCGHEGMAY 97
Cdd:TIGR01384   2 FCPKCGSLmTPKNG---VYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETII---IREEDSETLPTTRVECPKCGHKEAYY 75

                          90       100
                  ....*....|....*....|....*..
gi 71649339    98 HTRQMRSADEGQTVFYTCTNCKFQEKE 124
Cdd:TIGR01384  76 WLLQTRRADEPETRFYKCTKCGYVWRE 102

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 71649339  81 PVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKFQEKED 125
Cdd:cd10511   3 PTTKITCPKCGHDEAYWWMVQTRSADEPPTRFYKCTKCGHTWREY 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71649339    53 KVVKTSVVFHQLGTAmpmsveegpecQGPVVDR-RCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNC 118
Cdd:TIGR01385 237 EITKENLFEAQGAKI-----------QKAVTDLfTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEEC 292

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 71649339  86 RCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCK 119
Cdd:cd13749   9 KCGKCKKRKCTYYQLQTRSADEPMTTFVTCLNCG 42