1XPP,2PMZ


Conserved Protein Domain Family
RNAP_L

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cd06927: RNAP_L 
Click on image for an interactive view with Cn3D
L subunit of Archaeal RNA polymerase
The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is 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. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Statistics
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PSSM-Id: 132903
View PSSM: cd06927
Aligned: 34 rows
Threshold Bit Score: 64.1444
Threshold Setting Gi: 126465541
Created: 14-Nov-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:L- D heterodimer interface [polypeptide binding site]
Evidence:
  • 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
  • Comment:The assembly of the two largest RNAP subunits (A'/A" and B in archaea) depends on the presence of the L/D heterodimer.
  • Comment:The L subunit interfaces with the RPB11-like domain of the D subunit.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #                ## #  ##      #                                                
1XPP_A        13 LRVISKEKNSITVEMINYDNTLLRTLVEEILKdDQVDEARYYIKHPVi-----------DNPQIYVRVKs--gKPQSAIK 79  Thermoplasma ac...
2PMZ_L         3 IRILKSESNYLELEIEGEDHTLGNLIAGTLRRiSGVSFASYYQPHPLs-----------DKIIVKILTDgs-iTPKDALL 70  Sulfolobus solf...
Q8TZ81         8 VVVKKYDKDEVLLELPGEDHTLCNLLRWALNR-QDGIIATYRIEHPIlgkehkvdeeryVPPKMRIRAVdedaDAREALE 86  Methanopyrus ka...
Q9YEZ1         4 LRIIRESRGSYVIQVYGEDHTLGTLLVEAIKRvSNPKLAYYEAVHPMe-----------DIIQVYVKYEdd-vDIKEVLR 71  Aeropyrum pernix
Q74MN9         8 VKILEETDNLIKVQFKGETHTLFNALKEIAYTiNGVKKAAYFIEHPLk-----------DNNYFIIETDgs-iKARDALI 75  Nanoarchaeum eq...
YP_001273929   8 IEIIEDKTLELEFIVHGESHGVCNALRHILMQdSDVEYAVYNIDHPLt-----------GEPNMTIKTKrg-kRPRKVLK 75  Methanobrevibac...
NP_069045      3 VKIIDIGEDYVRLVIKGEGHTYLNLLQHYLVEdEDVIVARYNIPHPLi-----------GEPEIYIKTSg--vDPLEAVK 69  Archaeoglobus f...
Q8ZW46         7 LEILKLDDKYLELKAKGETYTLFSPLVEYLSNdPDVEYVQFDVDHPLq-----------ENAYFKLKVKr--gNPLEAIQ 73  Pyrobaculum aer...
YP_001541352   6 VKSIKLSGDYMEVTVEGEDYTVMSPLLTYILQdPEVEFATFDMDHPLl-----------RNITLKLRTKg--kDPLKVLE 72  Caldivirga maqu...
NP_276434      1 MEVILDKRNEMEIVFEGETHTLCNVLRSILMEdEKVKAAAYSIDHPIv-----------GEPQLYIRAG----SPKKSLK 65  Methanothermoba...
Feature 1          #   # ##  ## 
1XPP_A        80 RAVRKLSKLYEDLGT 94  Thermoplasma acidophilum
2PMZ_L        71 KAIENIRGMTSHYID 85  Sulfolobus solfataricus
Q8TZ81        87 RAIEELLELVEEAKE 101 Methanopyrus kandleri
Q9YEZ1        72 KASDYLLEVIGDFRR 86  Aeropyrum pernix
Q74MN9        76 QALKKLKEELLNFKD 90  Nanoarchaeum equitans
YP_001273929  76 KAASQLKDDAADFKK 90  Methanobrevibacter smithii ATCC 35061
NP_069045     70 RANEKIIAACNTLLE 84  Archaeoglobus fulgidus DSM 4304
Q8ZW46        74 RAVNAILSDLEELER 88  Pyrobaculum aerophilum
YP_001541352  73 DAVNRILNDIGELEG 87  Caldivirga maquilingensis IC-167
NP_276434     66 AAAETLRDRCDEFRR 80  Methanothermobacter thermautotrophicus str. Delta H

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