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Conserved domains on  [gi|1500418699|ref|WP_121958625|]
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RNA 2',3'-cyclic phosphodiesterase [Petrotoga sp. 9PWA.NaAc.5.4]

Protein Classification

2'-5' RNA ligase family protein( domain architecture ID 11445567)

2'-5' RNA ligase family protein similar to RNA 2',3'-cyclic phosphodiesterase hydrolyzes RNA 2',3'-cyclic phosphodiester to the RNA 2'-phosphomonoester

CATH:  3.90.1140.10
EC:  3.1.4.58
Gene Ontology:  GO:0004113|GO:0008664
PubMed:  25239919|8940112
SCOP:  4000652

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 17-197 8.84e-44

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 144.40  E-value: 8.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  17 RSFIAIETNKELEKGISDLIEKLKRmGFKANWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERLTGFPTFIFKIQRIGFF 96
Cdd:COG1514     2 RLFIALPPPEELREALAALRARLKA-APGGRWVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAPPFELRLDGLGAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  97 ENNNvPRVLWLGIKDDPTLVGLYEEVKKVIKINEIDTKEGDFVPHITVGRIKGYPNHWQELLNSL-DFEEIKVFVNSIGI 175
Cdd:COG1514    81 PRPR-PRVLWLGVEPSPELLALHRRLRAALARAGLPPERRPFVPHVTLARGKRPAPPLAPALAELrDFEFPEFTVDEFVL 159

                         170       180
                  ....*....|....*....|..
gi 1500418699 176 YSSTLTKKRPIYNKLYTVDFEG 197
Cdd:COG1514   160 YESELTPDGPRYEVLAEFPLGG 181
 
Name Accession Description Interval E-value
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 17-197 8.84e-44

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 144.40  E-value: 8.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  17 RSFIAIETNKELEKGISDLIEKLKRmGFKANWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERLTGFPTFIFKIQRIGFF 96
Cdd:COG1514     2 RLFIALPPPEELREALAALRARLKA-APGGRWVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAPPFELRLDGLGAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  97 ENNNvPRVLWLGIKDDPTLVGLYEEVKKVIKINEIDTKEGDFVPHITVGRIKGYPNHWQELLNSL-DFEEIKVFVNSIGI 175
Cdd:COG1514    81 PRPR-PRVLWLGVEPSPELLALHRRLRAALARAGLPPERRPFVPHVTLARGKRPAPPLAPALAELrDFEFPEFTVDEFVL 159

                         170       180
                  ....*....|....*....|..
gi 1500418699 176 YSSTLTKKRPIYNKLYTVDFEG 197
Cdd:COG1514   160 YESELTPDGPRYEVLAEFPLGG 181
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 16-193 7.71e-42

2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. [Transcription, RNA processing]


Pssm-ID: 274058 [Multi-domain]  Cd Length: 179  Bit Score: 139.34  E-value: 7.71e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  16 VRSFIAIETNKELEKGISDLIEKLKRMGFKANWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERltGFPTFIFKIQRIGF 95
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI--AEPPFTLKLEGIGV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  96 FENNNVPRVLWLGIKDDPTLVGLYEEVKKVIKINEIDTKEGDFVPHITVGRIKGYPNHWQELLNSLDFEEIKVF-VNSIG 174
Cdd:TIGR02258  79 FGNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKPGVPEFLQEFANEEFGSFhVDEFH 158

                         170
                  ....*....|....*....
gi 1500418699 175 IYSSTLTKKRPIYNKLYTV 193
Cdd:TIGR02258 159 LYSSTLTPGGPIYEPLARF 177
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 22-106 3.83e-10

LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.


Pssm-ID: 397118 [Multi-domain]  Cd Length: 87  Bit Score: 54.34  E-value: 3.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  22 IETNKELEKGISDLIEKLKR----MGFKanWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERLTGFPTFIFKIQRIGFFE 97
Cdd:pfam02834   1 LGPPEEIAEELARLRAELERalakLGFK--PVRPFNPHITLAFLGEVDEEKLPELLEALAEIAFGFPPFELKVDGVGLFP 78


                  ....*....
gi 1500418699  98 NNNVPRVLW 106
Cdd:pfam02834  79 SRLRPRVIY 87
PRK13679 PRK13679
hypothetical protein; Provisional
 55-146 3.67e-04

hypothetical protein; Provisional


Pssm-ID: 184236  Cd Length: 168  Bit Score: 39.54  E-value: 3.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  55 HLTL---FFLGDQKISKIAHlayKIGERLTGFPTFIFKIQRIG-FFENNNVprvLWLGIKDDPTLVGLYEevkkviKINE 130
Cdd:PRK13679   34 HITLkepFEISDEQLDSIVE---ELRAIASETKPFTLHVTKVSsFAPTNNV---IYFKVEKTEELEELHE------RLHS 101

                          90
                  ....*....|....*....
gi 1500418699 131 ID---TKEGDFVPHITVGR 146
Cdd:PRK13679  102 GDfygEAEYAFVPHITIGQ 120
 
Name Accession Description Interval E-value
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 17-197 8.84e-44

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 144.40  E-value: 8.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  17 RSFIAIETNKELEKGISDLIEKLKRmGFKANWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERLTGFPTFIFKIQRIGFF 96
Cdd:COG1514     2 RLFIALPPPEELREALAALRARLKA-APGGRWVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAPPFELRLDGLGAF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  97 ENNNvPRVLWLGIKDDPTLVGLYEEVKKVIKINEIDTKEGDFVPHITVGRIKGYPNHWQELLNSL-DFEEIKVFVNSIGI 175
Cdd:COG1514    81 PRPR-PRVLWLGVEPSPELLALHRRLRAALARAGLPPERRPFVPHVTLARGKRPAPPLAPALAELrDFEFPEFTVDEFVL 159

                         170       180
                  ....*....|....*....|..
gi 1500418699 176 YSSTLTKKRPIYNKLYTVDFEG 197
Cdd:COG1514   160 YESELTPDGPRYEVLAEFPLGG 181
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 16-193 7.71e-42

2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. [Transcription, RNA processing]


Pssm-ID: 274058 [Multi-domain]  Cd Length: 179  Bit Score: 139.34  E-value: 7.71e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  16 VRSFIAIETNKELEKGISDLIEKLKRMGFKANWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERltGFPTFIFKIQRIGF 95
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI--AEPPFTLKLEGIGV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  96 FENNNVPRVLWLGIKDDPTLVGLYEEVKKVIKINEIDTKEGDFVPHITVGRIKGYPNHWQELLNSLDFEEIKVF-VNSIG 174
Cdd:TIGR02258  79 FGNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKPGVPEFLQEFANEEFGSFhVDEFH 158

                         170
                  ....*....|....*....
gi 1500418699 175 IYSSTLTKKRPIYNKLYTV 193
Cdd:TIGR02258 159 LYSSTLTPGGPIYEPLARF 177
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 22-106 3.83e-10

LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.


Pssm-ID: 397118 [Multi-domain]  Cd Length: 87  Bit Score: 54.34  E-value: 3.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  22 IETNKELEKGISDLIEKLKR----MGFKanWTQAKNVHLTLFFLGDQKISKIAHLAYKIGERLTGFPTFIFKIQRIGFFE 97
Cdd:pfam02834   1 LGPPEEIAEELARLRAELERalakLGFK--PVRPFNPHITLAFLGEVDEEKLPELLEALAEIAFGFPPFELKVDGVGLFP 78


                  ....*....
gi 1500418699  98 NNNVPRVLW 106
Cdd:pfam02834  79 SRLRPRVIY 87
2_5_RNA_ligase2 pfam13563
2'-5' RNA ligase superfamily; This family contains proteins related to pfam02834. These ...
 55-146 1.86e-09

2'-5' RNA ligase superfamily; This family contains proteins related to pfam02834. These proteins are likely to be enzymes, but they may not share the RNA ligase activity.


Pssm-ID: 433312 [Multi-domain]  Cd Length: 152  Bit Score: 53.97  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  55 HLTLF--FLGDQKISKIAHLaykIGERLTGFPTFIFKIQRIGFFENNNvpRVLWLGIKDDPTLVGLYEEVKKVIKINEID 132
Cdd:pfam13563  27 HITLLypFVPDELLPELLEA---LAEVAAETEPFELTLGGFGTFGHRG--GVVYLSVEGSEPLRALHAALREALPPCLLK 101

                          90
                  ....*....|....
gi 1500418699 133 TKEGDFVPHITVGR 146
Cdd:pfam13563 102 QDSGPFTPHLTIAY 115
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 19-166 1.61e-04

AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function.


Pssm-ID: 402204 [Multi-domain]  Cd Length: 207  Bit Score: 41.10  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  19 FIAIE-TNKELEKGISDLIEKLKRM--GFKAN-WTQAKNVHLTLFFL---GDQKISKIAHLAYKIGERLT---GFPTFIF 88
Cdd:pfam10469   4 FLSIPlNSPELRKRLEEFQESVLKQlpGLDESlFIPPEKLHITLLVLvllDDEEVARAKEALRECREEIKdilNGNPLSL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  89 KIQRIGFFenNNVP---RVLWLGIKDD---PTLVGLYEEVKKVIKINEIDTKEG--DFVPHITVGRIKGYPNHWQELLNS 160
Cdd:pfam10469  84 RFKGLETF--NDDPsavRVLYAKVEEDdhsPKLQELADRIIRRFQEAGLLVKENnsRVKLHMTLMNTRYRKKKYAKSKES 161


                  ....*.
gi 1500418699 161 LDFEEI 166
Cdd:pfam10469 162 FDAREI 167
PRK13679 PRK13679
hypothetical protein; Provisional
 55-146 3.67e-04

hypothetical protein; Provisional


Pssm-ID: 184236  Cd Length: 168  Bit Score: 39.54  E-value: 3.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699  55 HLTL---FFLGDQKISKIAHlayKIGERLTGFPTFIFKIQRIG-FFENNNVprvLWLGIKDDPTLVGLYEevkkviKINE 130
Cdd:PRK13679   34 HITLkepFEISDEQLDSIVE---ELRAIASETKPFTLHVTKVSsFAPTNNV---IYFKVEKTEELEELHE------RLHS 101

                          90
                  ....*....|....*....
gi 1500418699 131 ID---TKEGDFVPHITVGR 146
Cdd:PRK13679  102 GDfygEAEYAFVPHITIGQ 120
PRK15124 PRK15124
RNA 2',3'-cyclic phosphodiesterase;
51-113 8.51e-04

RNA 2',3'-cyclic phosphodiesterase;


Pssm-ID: 185079  Cd Length: 176  Bit Score: 38.50  E-value: 8.51e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1500418699  51 AKNVHLTLFFLGD---QKISKIAHLAYKIGErltgfPTFIFKIQRIGFFENnnvPRVLWLGIKDDP 113
Cdd:PRK15124   39 AANLHLTLAFLGEvsaEKQQALSQLAGRIRQ-----PGFTLTLDDAGQWPR---SRVVWLGMRQPP 96
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 134-187 4.72e-03

LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.


Pssm-ID: 397118 [Multi-domain]  Cd Length: 87  Bit Score: 35.08  E-value: 4.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1500418699 134 KEGDFVPHITVGRIKGYPNH-WQELLNSLD-----FEEIKVFVNSIGIYSSTLtKKRPIY 187
Cdd:pfam02834  29 PVRPFNPHITLAFLGEVDEEkLPELLEALAeiafgFPPFELKVDGVGLFPSRL-RPRVIY 87
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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