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Conserved domains on  [gi|80973342|gb|ABB53412|]
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RNA polymerase II largest subunit, partial [Tetracentron sinense]

Protein Classification

DNA-directed RNA polymerase II subunit RPB1( domain architecture ID 10523289)

DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-227 8.41e-94

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


:

Pssm-ID: 461511  Cd Length: 188  Bit Score: 272.84  E-value: 8.41e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342    43 MDAVWIETQKLDSLKMKKSEFDKVFRYEIDNENWN--PSYMLPEHVEDLKTIREFRNVFDAEVQKLAADRCQLGTEIATT 120
Cdd:pfam04992   1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSGflPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREIIFPT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342   121 GDNSWP-MPVNLKRLIWNAQKTFKVDLRRPSDMHPMEIVEAVDKLQERLKVVPGDDLMSMEAQKNATLFFNILLRSTFAS 199
Cdd:pfam04992  81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160

                         170       180
                  ....*....|....*....|....*...
gi 80973342   200 KRVLKEYRLTREAFEWVIGEIESRFLQS 227
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNAP_largest_subunit_N super family cl19114
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 1-44 1.46e-17

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


The actual alignment was detected with superfamily member cd02582:

Pssm-ID: 473139 [Multi-domain]  Cd Length: 861  Bit Score: 81.14  E-value: 1.46e-17
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 80973342   1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMD 44
Cdd:cd02582 810 TSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVD 853
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-227 8.41e-94

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 272.84  E-value: 8.41e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342    43 MDAVWIETQKLDSLKMKKSEFDKVFRYEIDNENWN--PSYMLPEHVEDLKTIREFRNVFDAEVQKLAADRCQLGTEIATT 120
Cdd:pfam04992   1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSGflPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREIIFPT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342   121 GDNSWP-MPVNLKRLIWNAQKTFKVDLRRPSDMHPMEIVEAVDKLQERLKVVPGDDLMSMEAQKNATLFFNILLRSTFAS 199
Cdd:pfam04992  81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160

                         170       180
                  ....*....|....*....|....*...
gi 80973342   200 KRVLKEYRLTREAFEWVIGEIESRFLQS 227
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-44 1.46e-17

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 81.14  E-value: 1.46e-17
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 80973342   1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMD 44
Cdd:cd02582 810 TSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVD 853
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 1-44 2.59e-17

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 80.67  E-value: 2.59e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 80973342    1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMD 44
Cdd:PRK08566 814 TSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVD 857
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-195 2.02e-14

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 72.37  E-value: 2.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342     1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDAvwietQKLDSlkmkksefdkvfryeidNENWNPSY 80
Cdd:PRK14977  850 TEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDP-----QKLDH-----------------GEAFNLER 907

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342    81 MlpehVEDLKTIREFRNVFDAEVQKLAADrcqlgteiaTTGDNSWPMPVNLKRLIWNAqktfkvdlrRPSDMHPMEIVEA 160
Cdd:PRK14977  908 I----IEKQKIEDRGKGASKDEIEELAKE---------YTKTFNANLPKLLADAIHGA---------ELKEDELEAICAE 965

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 80973342   161 VDKLQERLKVVPGDDLMSMEAQKNATLFFNILLRS 195
Cdd:PRK14977  966 GKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRT 1000
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 206-240 3.90e-14

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 70.70  E-value: 3.90e-14
                        10        20        30
                ....*....|....*....|....*....|....*
gi 80973342 206 YRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAA 240
Cdd:cd02584   1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAA 35
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-227 8.41e-94

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 272.84  E-value: 8.41e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342    43 MDAVWIETQKLDSLKMKKSEFDKVFRYEIDNENWN--PSYMLPEHVEDLKTIREFRNVFDAEVQKLAADRCQLGTEIATT 120
Cdd:pfam04992   1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSGflPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREIIFPT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342   121 GDNSWP-MPVNLKRLIWNAQKTFKVDLRRPSDMHPMEIVEAVDKLQERLKVVPGDDLMSMEAQKNATLFFNILLRSTFAS 199
Cdd:pfam04992  81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160

                         170       180
                  ....*....|....*....|....*...
gi 80973342   200 KRVLKEYRLTREAFEWVIGEIESRFLQS 227
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-240 1.56e-43

RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.


Pssm-ID: 398596 [Multi-domain]  Cd Length: 516  Bit Score: 153.28  E-value: 1.56e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342     1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDAVWIETQKLDSLKMKKSEFDKVFRYeidnenwnpsy 80
Cdd:pfam04998  25 TAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTIEFSDLKLEDKFKN----------- 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342    81 mlpEHVEDLKTIREFRNvfdaevqklaadrcqlgteiattgdnswpmpvnlkrliwnaqktfkvdlrrpsdMHPMEIVEA 160
Cdd:pfam04998  94 ---DLLDDLLLLSEFSL------------------------------------------------------SYKKEILVR 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342   161 VDKLqerlkvvpGDDLMSMEAQKNATLFFNILLRSTFASKRVLKEYRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAA 240
Cdd:pfam04998 117 DSKL--------GRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAA 188
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-44 1.46e-17

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 81.14  E-value: 1.46e-17
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 80973342   1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMD 44
Cdd:cd02582 810 TSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVD 853
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 1-44 2.59e-17

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 80.67  E-value: 2.59e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 80973342    1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMD 44
Cdd:PRK08566 814 TSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVD 857
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-195 2.02e-14

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 72.37  E-value: 2.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342     1 TSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDAvwietQKLDSlkmkksefdkvfryeidNENWNPSY 80
Cdd:PRK14977  850 TEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDP-----QKLDH-----------------GEAFNLER 907

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 80973342    81 MlpehVEDLKTIREFRNVFDAEVQKLAADrcqlgteiaTTGDNSWPMPVNLKRLIWNAqktfkvdlrRPSDMHPMEIVEA 160
Cdd:PRK14977  908 I----IEKQKIEDRGKGASKDEIEELAKE---------YTKTFNANLPKLLADAIHGA---------ELKEDELEAICAE 965

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 80973342   161 VDKLQERLKVVPGDDLMSMEAQKNATLFFNILLRS 195
Cdd:PRK14977  966 GKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRT 1000
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 206-240 3.90e-14

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 70.70  E-value: 3.90e-14
                        10        20        30
                ....*....|....*....|....*....|....*
gi 80973342 206 YRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAA 240
Cdd:cd02584   1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAA 35
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 1-23 7.40e-13

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 67.56  E-value: 7.40e-13
                        10        20
                ....*....|....*....|...
gi 80973342   1 TSETGYIQRRLVKAMEDIMVKYD 23
Cdd:cd02733 729 TAETGYIQRRLVKAMEDVMVKYD 751
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 1-27 7.23e-12

Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259847 [Multi-domain]  Cd Length: 816  Bit Score: 64.49  E-value: 7.23e-12
                        10        20
                ....*....|....*....|....*..
gi 80973342   1 TSETGYIQRRLVKAMEDIMVKYDGTVR 27
Cdd:cd02583 790 TAETGYMQRRLMKALEDLSVQYDGTVR 816
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 1-23 7.82e-06

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


Pssm-ID: 259843 [Multi-domain]  Cd Length: 528  Bit Score: 46.27  E-value: 7.82e-06
                        10        20
                ....*....|....*....|...
gi 80973342   1 TSETGYIQRRLVKAMEDIMVKYD 23
Cdd:cd00399 506 TAESGYLQRRLVKALEDLVVHYD 528
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 203-240 6.79e-04

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 40.21  E-value: 6.79e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 80973342  203 LKEYRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAA 240
Cdd:PRK04309  30 LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAA 67
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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