2IGI,2GBZ,1J9A,1YTA


Conserved Protein Domain Family
Orn

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cd06135: Orn 
Click on image for an interactive view with Cn3D
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins
Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Statistics
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PSSM-Id: 99838
View PSSM: cd06135
Aligned: 60 rows
Threshold Bit Score: 173.116
Threshold Setting Gi: 46190895
Created: 9-Jan-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:putative active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1            #### #                                                                      
2IGI_A         7 LIWIDLEMTGLDp---------eRDRIIEIATLVTDAnLNILAEGPTIAVHQSd-----eQLALMDDWNVRTHTASGLVE 72  Escherichia coli
YP_001138799   7 FIGLDLETTGLDa---------hSGVILEVGIIIFDDdLMPIAARSWLTNELVe-----kESIVSAPVVEVMHEESGLWE 72  Corynebacterium...
ZP_01875273    4 LFWIDMEMTGLDp---------dENRILEIAILITDH-KLDIIDRFHAVIRTPk-----aILDGMDEWNTRTHTSNGLVK 68  Lentisphaera ar...
YP_001364968   5 FLFGDLETGGLNgrldngmlgmeYYPIFELAFIVTDSeLNQVGEALHIVVHQDd-----eHIARSHEWAIDVHTKSGLLA 79  Shewanella balt...
ZP_01461207    8 FVWLDLEMTGLDp---------eTCAIIEIGVIITGP-DLVPLAEIERVIWQPe-----eALARMEPVVREMHTRNGLLT 72  Stigmatella aur...
YP_001202064  13 LPWLDLETTGFTelfd---rrvyEHRILEIGAVVTDE-HFTVLASTSIVIQQPmv----rVLELSDEAVTRMHTNNGLFD 84  Pseudomonas flu...
ZP_02835733   10 ILWVDYEATGLMsd--------pFTVPLEGAAIITDGqLNELAVLEGITIHATe-----eELAYMGDFVRDMHTKTGLLD 76  Arthrobacter ch...
NP_968245      4 LFWIDMEMTGLDv---------eKEVIIEVAAIVTDL-NFKELETFETVVKQPq-----kYLDSMDAWNTEHHKKSGLTA 68  Bdellovibrio ba...
ZP_01810755   13 LLWLDLEMTGLDp---------qRDRVLEVAAIATDW-NFEEMAVIESVVHQSp-----kVLDLMDDWVRSQHASSGLTE 77  candidate divis...
ZP_02544629    6 ILWVDLEMTGLDp---------tKDKILEVAAIATDW-DFNEVGRFESAVKVDdslisarFKAGHNFWDANPDARDGLIL 75  candidate divis...
Feature 1                                                     ## ###                             
2IGI_A        73 RVk-aSTMGDREAELATLEFLKQwv-----------pAGKSPICGNSIGQDRRFLFKYMPELEAYFHYRYLDVSTLKELA 140 Escherichia coli
YP_001138799  73 DLktgHTQPLRQVEAEASAWILEa------------gANKLPMLGSSVTFDRTWLDHHMPQLHRMFHYRSVDATSVLLAS 140 Corynebacterium...
ZP_01875273   69 EAv--NGRFIQEVEIDLLNLADKhf-----------aNKQIFLCGSSLSLDRMFIEKFMPSFAKKLHYRIVDVSSWKAIF 135 Lentisphaera ar...
YP_001364968  80 AVr-aSSVSLAQAEQMVLEHLKAlgipk----hdrkaKTGVVFAGNSIMLDRSFIMCQMPELHEYMHYRQLDISALGLAA 154 Shewanella balt...
ZP_01461207   73 KVr-aSTTSLRVAERDVMALVASyc-----------aLGEGILCGNSIHTDRRFLIRYMPMLERFLHYRMVDVTSLKVLS 140 Stigmatella aur...
YP_001202064  85 EVv-kSFTTLKAAEHQLIQFYRQng----------vsKKVEPLCGSGIHFDRMFIEAQMPELHDFLYYRNLDISSVKEFL 153 Pseudomonas flu...
ZP_02835733   77 KVr-aSTVTRDQFDNALASFAAPyfptkgeeladgtkYRGMVIGGNSVKFDFDVTEKFFPQTRKNMDYRVIDISGLGELV 155 Arthrobacter ch...
NP_968245     69 KVp--NGMDPDQVEAKLVDMVKKhfp---------dpKDKPVLAGNSIMQDRLFINKYMPEFAGRLHYRMVDVSSWKVII 137 Bdellovibrio ba...
ZP_01810755   78 RVr-aSDVSETDAEDILLQFIDSvy----------kdGDPVVLAGNSIHQDRRFIRQYWQRLDARLHYRMLDVSAWKVVF 146 candidate divis...
ZP_02544629   76 QNs-qAKLTSKQVEEDILKFTKEyf----------thDEPILLAGNSIHQDRKFIDREWPNLGSLLHYRMLDVSAWKVVF 144 candidate divis...
Feature 1                                       #    #                
2IGI_A       141 RRWKPeil---------------dgfTKQGTHQAMDDIRESVAELAYYREHFI 178 Escherichia coli
YP_001138799 141 TSLYDfinindqqtllvldmlehlkrWDLKPHRALYDLCQSAALVKATLNAVA 193 Corynebacterium glutamicum R
ZP_01875273  136 QTFLDlr------------------fHKQDAHRAMNDIEESLRELKLYLSYID 170 Lentisphaera araneosa HTCC2155
YP_001364968 155 RAWAPever-------------naikAKQYQHEALADIRESIAELKYYRDELF 194 Shewanella baltica OS185
ZP_01461207  141 RAWYPevf---------------eprKGSAGHTALADIRASITELSFYRDTFF 178 Stigmatella aurantiaca DW4/3-1
YP_001202064 154 KTISPsf-----------------epSKRQQHRALPDILESVAEAKTYRALLA 189 Pseudomonas fluorescens SBW25
ZP_02835733  156 RRWSYdywk--------------ampPKLSDHTALTDIRAGVNELRYYRAGMH 194 Arthrobacter chlorophenolicus A6
NP_968245    138 NNKFKyv------------------yQKANKHRALEDIRESIQELRHYTDKMH 172 Bdellovibrio bacteriovorus HD100
ZP_01810755  147 EGKYQkr------------------fPKPEDHRALEDIRGSIMELKYYLTKVR 181 candidate division TM7 genomosp. GTL1
ZP_02544629  145 DGKYGkr------------------fAKPEAHRALDDIKGSIMELKYYLTKVR 179 candidate division TM7 single-cell isolate...

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