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: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        #                ## #  ##      #                                                
1XPP_A        13 LRVISKEKNSITVEMINYDNTLLRTLVEEILKdDQVDEARYYIKHPVi-----------DNPQIYVRVKs--gKPQSAIK 79
2PMZ_L         3 IRILKSESNYLELEIEGEDHTLGNLIAGTLRRiSGVSFASYYQPHPLs-----------DKIIVKILTDgs-iTPKDALL 70
gi 23822101    8 VVVKKYDKDEVLLELPGEDHTLCNLLRWALNR-QDGIIATYRIEHPIlgkehkvdeeryVPPKMRIRAVdedaDAREALE 86
gi 150421655   4 LRIIRESRGSYVIQVYGEDHTLGTLLVEAIKRvSNPKLAYYEAVHPMe-----------DIIQVYVKYEdd-vDIKEVLR 71
gi 55976463    8 VKILEETDNLIKVQFKGETHTLFNALKEIAYTiNGVKKAAYFIEHPLk-----------DNNYFIIETDgs-iKARDALI 75
gi 148643416   8 IEIIEDKTLELEFIVHGESHGVCNALRHILMQdSDVEYAVYNIDHPLt-----------GEPNMTIKTKrg-kRPRKVLK 75
gi 11497823    3 VKIIDIGEDYVRLVIKGEGHTYLNLLQHYLVEdEDVIVARYNIPHPLi-----------GEPEIYIKTSg--vDPLEAVK 69
gi 21263946    7 LEILKLDDKYLELKAKGETYTLFSPLVEYLSNdPDVEYVQFDVDHPLq-----------ENAYFKLKVKr--gNPLEAIQ 73
gi 159042100   6 VKSIKLSGDYMEVTVEGEDYTVMSPLLTYILQdPEVEFATFDMDHPLl-----------RNITLKLRTKg--kDPLKVLE 72
gi 15679317    1 MEVILDKRNEMEIVFEGETHTLCNVLRSILMEdEKVKAAAYSIDHPIv-----------GEPQLYIRAG----SPKKSLK 65
                         90
                 ....*....|....*
Feature 1          #   # ##  ## 
1XPP_A        80 RAVRKLSKLYEDLGT 94
2PMZ_L        71 KAIENIRGMTSHYID 85
gi 23822101   87 RAIEELLELVEEAKE 101
gi 150421655  72 KASDYLLEVIGDFRR 86
gi 55976463   76 QALKKLKEELLNFKD 90
gi 148643416  76 KAASQLKDDAADFKK 90
gi 11497823   70 RANEKIIAACNTLLE 84
gi 21263946   74 RAVNAILSDLEELER 88
gi 159042100  73 DAVNRILNDIGELEG 87
gi 15679317   66 AAAETLRDRCDEFRR 80

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