3MDG,3P5T,3BHO,2CL3,2J8Q,3Q2S,3BAP


Conserved Protein Domain Family
NUDIX_Cfim25_Nudt21

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cd18871: NUDIX_Cfim25_Nudt21 
25 kDa subunit of cleavage factor Im
Precursor mRNA (pre-mRNA) cleavage factor I(m) (also called NUDIX (nucleoside diphosphate linked moiety X))-type motif 21) is a oligomer composed of a small 25 kDa subunit (CF I(m)25) and a variable larger subunit of either 59, 68 or 72 kDa and plays an important role in pre-mRNA 3'-end cleavage and the selection of poly(A) sites in a 3'-untranslated region (3'-UTR) of mRNA, producing mRNAs with variable 3' ends. The small subunit also interacts with RNA, poly(A) polymerase, and the nuclear poly(A)-binding protein and belongs to the NUDIX hydrolase superfamily. NUDIX hydrolases are found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes.
Statistics
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PSSM-Id: 467583
Aligned: 39 rows
Threshold Bit Score: 227.495
Created: 29-Nov-2010
Updated: 27-Apr-2023
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:3BOH: Homo sapiens 25 kDa subunit of cleavage factor Im, contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                              #                                              #       
3MDG_A     39 LYPLTNYTFGTKePLYEKDSs-VAARFQRMREEFDKi-GMRRTVEGVLIVHEHRLPHVLLLQLGt------TFFKLPGGE 110 human
3BHO_A     20 LYPLTNYTFGTKePLYEKDSs-VAARFQRMREEFDKi-GMRRTVEGVLIVHEHRLPHVLLLQLGt------TFFKLPGGE 91  human
EFN55436    1 VYPVGNYTFGSKpPKFEKDSs-VTQRLERLKEKYARe-GLRRSVEAVLVVHEHGHPHVLVLQMGa------SFFKLPGGR 72  Chlorella variabilis
Q55E68      9 YNFNTSYSFGKE-EKKEKEQs-LTSKLARLKDSYEKe-GLRKAVEGIIIIHDHGHPHILLLQDN-------NYFKLPGGK 78  Dictyostelium disc...
EIE20931   10 IYPVANYNFGSKaAKTEKDTn-VQARLSRWEEKYKKe-GVRRSVDAVLLVWEHNHPHVLLLQLGt------SFFKLPGGR 81  Coccomyxa sp. C-169
EEH57450   13 VYPVTNYSFGQKaGRAAKDAt-PSATATRLREAYERd-GPRRSVDAVMLVNQHNTPHVLLLQSAgsgpgapATFRLPGGR 90  Micromonas pusilla...
ACO69562   22 VYPVSNYTFGSKaAKADKDAt-VAEAMIRYKDKYEKe-GMRRTVEAILLVNQHDHPHVLLLQRTmag--ggVEYKLPGGR 97  Micromonas sp. RCC299
EFC41954    9 IYDYTFIKWTKKnPQVEKDKs-VPERLKRLENNYLTh-GMKRTVEAAIAVNIHGHPHIMLLRIGns---qkGFHKLPGGR 83  Naegleria gruberi
EGD77564   10 IFPNSNYKILKDdSKTEPKSa-MDEKLMALMHKFNEt-GLVETMQLVMLVEQHGHPHVLLLQPHp------KFSLLPHTE 81  Salpingoeca sp. AT...
EAL49551   61 IYPIENYQIDKKeKLDKLKHqtFGYQMDQLKISVEKnhVPRTSVYGVILVHKNNFPHLLVLQSNlsm-dlkDEIHLVGGR 139 Entamoeba histolyt...
Feature 1                                                #    # #              #              
3MDG_A    111 LNP-GEDEVEGLKRLMTEILGRq---dGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQekALFA 186 human
3BHO_A     92 LNP-GEDEVEGLKRLMTEILGRq---dGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQekALFA 167 human
EFN55436   73 LRP-GEDEAEGMLRKLHSLLAPpa--eNMRPDWRVSDLLGTWWRPNFENMMYPYCPAHVARPKEVKRLFLIALPerCYLS 149 Chlorella variabilis
Q55E68     79 LKP-GENEIDGLIRKLTKKLSPtg-tpVSDAPWEIGDHVSTWWRPNFEPSLFPYIPSHITKPKECKKLFVVTLPekCKFA 156 Dictyostelium disc...
EIE20931   82 LRP-GEDEKMGLRRKLENNLSPea--aSLAHPWDIGQCIATYWRPNFDMTLYPYLPAHITRPKEVKKLYLISLPekCYLA 158 Coccomyxa sp. C-169
EEH57450   91 LRR-GEGELEGLQRKLHSKLSPsdaslGGAKEWETGDCLARWHRPAHDAHFYPYLPTHATRPKEARAVYAVQLPekCKFA 169 Micromonas pusilla...
ACO69562   98 LRH-GEGEVAGLQRKLHNKLSPse-qsLRIEHWECGDCVARWFRPAFEPNYYPYLPAHVTKPKESRTVYIAQLPerCKFC 175 Micromonas sp. RCC299
EFC41954   84 CRR-DETEEECLKRKLTKRLAPed-pnEIMPEWIVHGVVSVWYRPNFENSFYPYLPAHITKPKERKLIYLVTIPe-CTIA 160 Naegleria gruberi
EGD77564   82 IKP-DETSKETVHRILQEQFQVa---ePALNQFRIVDLAAVWWRPHFEQPTYPYQPPHVTKPKERIQVVLVQMPesCDFV 157 Salpingoeca sp. AT...
EAL49551  140 LKIgEDDPVEGLKRKLRKKMSM-----EYITHYEIGELLGTFYRIEYDKNLYPYIPVHVSQVKEIINIYMIHLVekCDFK 214 Entamoeba histolyt...
Feature 1                                        
3MDG_A    187 VPKNYKLVAAPLFELYDNapgYGPIISSLPQLLSR 221 human
3BHO_A    168 VPKNYKLVAAPLFELYDNapgYGPIISSLPQLLSR 202 human
EFN55436  150 VPKNMRLVAVPLFELYDNisrYGPVISSIPALLSR 184 Chlorella variabilis
Q55E68    157 VSNNLSLIAVSLYEIYNNsqrYGAVISSIPALISR 191 Dictyostelium discoideum
EIE20931  159 VPRNAKLIAVPLFELYENtarFGMVISALPHILSR 193 Coccomyxa sp. C-169
EEH57450  170 VPKSLKLLAVPLFELYGNekrYGAVVSSIPYLISR 204 Micromonas pusilla CCMP1545
ACO69562  176 VPKNLKLLAVPLFEMYANeakYGAVAASVPYLISR 210 Micromonas sp. RCC299
EFC41954  161 YPRNYDFIPMPFFDLYENskkFGSIISSLPQVISK 195 Naegleria gruberi
EGD77564  158 VPGNGNVRAVPLIELYDNkesFGQLIATLPQTLSR 192 Salpingoeca sp. ATCC50818
EAL49551  215 IFDTDKLSSIPLFALHNNfekYNITLCSIPTLVSR 249 Entamoeba histolytica HM-1:IMSS

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