1I50,1XPP,1IW7,1I50,2PMZ,1BDF,2PMZ,1IW7,1BDF


Conserved Protein Domain Family
RNAP_RPB11_RPB3

?
cd00460: RNAP_RPB11_RPB3 
Click on image for an interactive view with Cn3D
RPB11 and RPB3 subunits of RNA polymerase
The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal 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, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.
Statistics
?
PSSM-Id: 132901
View PSSM: cd00460
Aligned: 10 rows
Threshold Bit Score: 50.4966
Threshold Setting Gi: 167744884
Created: 6-Mar-2002
Updated: 17-Jan-2013
Structure
?
Program:
Drawing:
Aligned Rows:
 
dimer interface
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:dimer interface [polypeptide binding site]
Evidence:
  • Comment:The eukaryotic RNAP II RPB11 and RPB3 subunits form a heterodimer, which is involved in RNAP assembly. The dimer stabilizes the association of the two largest RNAP subunits, RPB1 and RPB2. In archaea, the equivalent dimer is composed of subunits L and D. In bacteria, the equivalent dimer is a homodimer of alpha subunits.
  • Comment:RPB11 (subunit L in archaea) interfaces with the RPB11-like subdomain of RPB3 (subunit D in archaea). The bacterial alpha subunit homodimerizes through its RPB11-like subdomain.
  • Structure:1I50; Saccharomyces cerevisiae RNAP II RPB11 subunit (1I50_K) heterodimerizes with RPB3 subunit (1I50_C); defined using 3.5A contacts.
    View structure with Cn3D
  • Structure:1PMZ_L: Sulfolobus solfataricus RNAP L subunit heterodimerizes with the D subunit (1PMZ_D), determined at 3.5 A contacts.
    View structure with Cn3D
  • Structure:1IW7_AB; Interface between two Thermus thermophilus RNAP alpha subunits, determined at 3.5A contacts.
    View structure with Cn3D
  • Structure:1BDF_AB; Interface between two Escherichia coli RNAP alpha subunits; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 9657722

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1       # #              #       # ##  #  #                                             
1I50_K       19 LKI-DPDtkapNAVVITFEKe----DHTLGNLIRAELLNd---------------------------------------- 53
1XPP_A       13 LRViSKEk---NSITVEMINy----DNTLLRTLVEEILKd---------------------------------------- 45
1IW7_A       11 FTV-RTQg--rEYGEFVLEPlergfGVTLGNPLRRILLSsipgtavtsvyiedvlhefstipgvkedvveiilnlkelvv 87
gi 82180681  14 VQA-QGNe--eSCVTFVLHEe----DHTLGNSLRYMVMKn---------------------------------------- 46
1I50_C        8 VKIrEASk---DNVDFILSNv----DLAMANSLRRVMIAeiptlaidsvevetnttvladefiahrlgliplqsmdieql 80
2PMZ_L        3 IRIlKSEs---NYLELEIEGe----DHTLGNLIAGTLRRi---------------------------------------- 35
1BDF_A       14 VDI-EQVs--sTHAKVTLEPlergfGHTLGNALRAILLSsmpgcavteveidgvlheystkegvqedileillnlkglav 90
2PMZ_D        3 INLlHKDd---TRIDLVFEGy----PLEFVNAIRRASMLyvpimavddvyfiennsplydeilahrlalipfmseealdt 75
1IW7_B       11 FTV-RTQg--rEYGEFVLEPlergfGVTLGNPLRRILLSsipgtavtsvyiedvlhefstipgvkedvveiilnlkelvv 87
1BDF_B       14 VDI-EQVs--sTHAKVTLEPlergfGHTLGNALRAILLSsmpgcavteveidgvlheystkegvqedileillnlkglav 90
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1I50_K          --------------------------------------------------------------------------------
1XPP_A          --------------------------------------------------------------------------------
1IW7_A       88 rflnpslqtvtlllkaegpkev------kardflpvadveimnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdr 161
gi 82180681     --------------------------------------------------------------------------------
1I50_C       81 eysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvivsnlmgrnighpiiqdkegngvlicklrkgqelkltcvak 160
2PMZ_L          --------------------------------------------------------------------------------
1BDF_A       91 rvqgkdeviltlnksgigpvtaa---dithdgdveivkpqhvichltdenasismrikvqrgrgyvpastrihseederp 167
2PMZ_D       76 yrwpeeciectencekcytk---------iyieaeapneprmiyskdiksedpsvvpisgdipivllgtnqkislearlr 146
1IW7_B       88 rflnpslqtvtlllkaegpkev------kardflpvadveimnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdr 161
1BDF_B       91 rvqgkdeviltlnksgigpvtaa---dithdgdveivkpqhvichltdenasismrikvqrgrgyvpastrihseederp 167
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1I50_K       54 ----------RKVLFAAYKVEHpf----------------------------------------------------fARF 71
1XPP_A       46 ----------DQVDEARYYIKHpv----------------------------------------------------iDNP 63
1IW7_A      162 inaipvdavfSPVRRVAFQVEDtrlgq----------------------------------------------rtdlDKL 195
gi 82180681  47 ----------PEVEFCGYSITHps----------------------------------------------------eTKI 64
1I50_C      161 kgiakehakwGPAAAIEFEYDPwnklkhtdywyeqdsakewpqs------------knceyedppnegdpfdykaqaDTF 228
2PMZ_L       36 ----------SGVSFASYYQPHpl----------------------------------------------------sDKI 53
1BDF_A      168 igrllvdacySPVERIAYNVEAarveq----------------------------------------------rtdlDKL 201
2PMZ_D      147 lgygkehakfIPVSLSVVRYYPkveilancekavnvcpegvfelkdgklsvknelsctlceeclrycngsirisfveDKY 226
1IW7_B      162 inaipvdavfSPVRRVAFQVEDtrlgq----------------------------------------------rtdlDKL 195
1BDF_B      168 igrllvdacySPVERIAYNVEAarveq----------------------------------------------rtdlDKL 201
                       250       260       270
                ....*....|....*....|....*....|
Feature 1                       #  #   # #####
1I50_K       72 KLRIQTTegyDPKDALKNACNSIINKLGAL 101
1XPP_A       64 QIYVRVKs-gKPQSAIKRAVRKLSKLYEDL 92
1IW7_A      196 TLRIWTDgsvTPLEALNQAVEILREHLTYF 225
gi 82180681  65 NFRIQTRngiPAVEPFRRGLNELVDVCQHV 94
1I50_C      229 YMNVESVgsiPVDQVVVRGIDTLQKKVASI 258
2PMZ_L       54 IVKILTDgsiTPKDALLKAIENIRGMTSHY 83
1BDF_A      202 VIEMETNgtiDPEEAIRRAATILAEQLEAF 231
2PMZ_D      227 ILEIESVgslKPERILLEAGKSIIRKIEEL 256
1IW7_B      196 TLRIWTDgsvTPLEALNQAVEILREHLTYF 225
1BDF_B      202 VIEMETNgtiDPEEAIRRAATILAEQLEAF 231

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap