NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|818607481|gb|KKS56439|]
View 

MAG: 2'-5' RNA ligase, LigT [Candidatus Magasanikbacteria bacterium GW2011_GWA2_42_32]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 4-202 2.55e-36

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


:

Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 125.14  E-value: 2.55e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   4 IRTFIAINIPRETKEEIGRTIENLgskfkKYSQDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLG 83
Cdd:COG1514    1 MRLFIALPPPEELREALAALRARL-----KAAPGGRWVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAPPFELRLD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481  84 DISYYytdKKGSDSVIYIGIVDPEkNISALYKTLAKQLRLSGFSPTNRI-DPHITIGRLaKRKDRQLQTEILDTISTSGT 162
Cdd:COG1514   76 GLGAF---PRPRPRVLWLGVEPSP-ELLALHRRLRAALARAGLPPERRPfVPHVTLARG-KRPAPPLAPALAELRDFEFP 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 818607481 163 TyvsspetgiVKVEKLYIYESISMPTQTKYRIIRSFNLSG 202
Cdd:COG1514  151 E---------FTVDEFVLYESELTPDGPRYEVLAEFPLGG 181
 
Name Accession Description Interval E-value
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 4-202 2.55e-36

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


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 125.14  E-value: 2.55e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   4 IRTFIAINIPRETKEEIGRTIENLgskfkKYSQDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLG 83
Cdd:COG1514    1 MRLFIALPPPEELREALAALRARL-----KAAPGGRWVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAPPFELRLD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481  84 DISYYytdKKGSDSVIYIGIVDPEkNISALYKTLAKQLRLSGFSPTNRI-DPHITIGRLaKRKDRQLQTEILDTISTSGT 162
Cdd:COG1514   76 GLGAF---PRPRPRVLWLGVEPSP-ELLALHRRLRAALARAGLPPERRPfVPHVTLARG-KRPAPPLAPALAELRDFEFP 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 818607481 163 TyvsspetgiVKVEKLYIYESISMPTQTKYRIIRSFNLSG 202
Cdd:COG1514  151 E---------FTVDEFVLYESELTPDGPRYEVLAEFPLGG 181
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 4-200 1.49e-33

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: 118.16  E-value: 1.49e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481    4 IRTFIAINIPRETKEEIGRTIENLgskfKKYSQDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAqsFPPFEIKLG 83
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKL----KSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   84 DISYYytDKKGSDSVIYIGiVDPEKNISALYKTLAKQLRLSGFSPTNR-IDPHITIGRLAKRKdrqlqTEILDTISTsgt 162
Cdd:TIGR02258  75 GIGVF--GNPKRPRVLWAG-VEQSEELTQLHADLERELAKLGFSKEERpFTPHITLARKKSGK-----PGVPEFLQE--- 143

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 818607481  163 tyVSSPETGIVKVEKLYIYESISMPTQTKYRIIRSFNL 200
Cdd:TIGR02258 144 --FANEEFGSFHVDEFHLYSSTLTPGGPIYEPLARFQL 179
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 10-100 2.42e-12

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: 60.12  E-value: 2.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   10 INIPRETKEEIGRTIENLGSKFKKYsqDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLGDISYYY 89
Cdd:pfam02834   1 LGPPEEIAEELARLRAELERALAKL--GFKPVRPFNPHITLAFLGEVDEEKLPELLEALAEIAFGFPPFELKVDGVGLFP 78

                          90
                  ....*....|.
gi 818607481   90 TDKKGsdSVIY 100
Cdd:pfam02834  79 SRLRP--RVIY 87
PRK13679 PRK13679
hypothetical protein; Provisional
 47-140 1.01e-05

hypothetical protein; Provisional


Pssm-ID: 184236  Cd Length: 168  Bit Score: 44.16  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481  47 HVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLGDISYYYTdkkgSDSVIYIGIVDPEKnISALYKTLAKQLrLSGf 126
Cdd:PRK13679  34 HITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAP----TNNVIYFKVEKTEE-LEELHERLHSGD-FYG- 106

                         90
                 ....*....|....
gi 818607481 127 SPTNRIDPHITIGR 140
Cdd:PRK13679 107 EAEYAFVPHITIGQ 120
 
Name Accession Description Interval E-value
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 4-202 2.55e-36

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


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 125.14  E-value: 2.55e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   4 IRTFIAINIPRETKEEIGRTIENLgskfkKYSQDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLG 83
Cdd:COG1514    1 MRLFIALPPPEELREALAALRARL-----KAAPGGRWVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAPPFELRLD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481  84 DISYYytdKKGSDSVIYIGIVDPEkNISALYKTLAKQLRLSGFSPTNRI-DPHITIGRLaKRKDRQLQTEILDTISTSGT 162
Cdd:COG1514   76 GLGAF---PRPRPRVLWLGVEPSP-ELLALHRRLRAALARAGLPPERRPfVPHVTLARG-KRPAPPLAPALAELRDFEFP 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 818607481 163 TyvsspetgiVKVEKLYIYESISMPTQTKYRIIRSFNLSG 202
Cdd:COG1514  151 E---------FTVDEFVLYESELTPDGPRYEVLAEFPLGG 181
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 4-200 1.49e-33

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: 118.16  E-value: 1.49e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481    4 IRTFIAINIPRETKEEIGRTIENLgskfKKYSQDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAqsFPPFEIKLG 83
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKL----KSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   84 DISYYytDKKGSDSVIYIGiVDPEKNISALYKTLAKQLRLSGFSPTNR-IDPHITIGRLAKRKdrqlqTEILDTISTsgt 162
Cdd:TIGR02258  75 GIGVF--GNPKRPRVLWAG-VEQSEELTQLHADLERELAKLGFSKEERpFTPHITLARKKSGK-----PGVPEFLQE--- 143

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 818607481  163 tyVSSPETGIVKVEKLYIYESISMPTQTKYRIIRSFNL 200
Cdd:TIGR02258 144 --FANEEFGSFHVDEFHLYSSTLTPGGPIYEPLARFQL 179
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 10-100 2.42e-12

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: 60.12  E-value: 2.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   10 INIPRETKEEIGRTIENLGSKFKKYsqDLKWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLGDISYYY 89
Cdd:pfam02834   1 LGPPEEIAEELARLRAELERALAKL--GFKPVRPFNPHITLAFLGEVDEEKLPELLEALAEIAFGFPPFELKVDGVGLFP 78

                          90
                  ....*....|.
gi 818607481   90 TDKKGsdSVIY 100
Cdd:pfam02834  79 SRLRP--RVIY 87
2_5_RNA_ligase2 pfam13563
2'-5' RNA ligase superfamily; This family contains proteins related to pfam02834. These ...
 46-148 5.80e-10

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: 55.51  E-value: 5.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481   46 LHVTLSFQGSITlEDIATLEETVEKVAQSFPPFEIKLGDISYYytdkKGSDSVIYIGiVDPEKNISALYKTLAKQLRLSG 125
Cdd:pfam13563  26 PHITLLYPFVPD-ELLPELLEALAEVAAETEPFELTLGGFGTF----GHRGGVVYLS-VEGSEPLRALHAALREALPPCL 99

                          90       100
                  ....*....|....*....|....
gi 818607481  126 F-SPTNRIDPHITIGRLAKRKDRQ 148
Cdd:pfam13563 100 LkQDSGPFTPHLTIAYKVDDAPAA 123
PRK13679 PRK13679
hypothetical protein; Provisional
 47-140 1.01e-05

hypothetical protein; Provisional


Pssm-ID: 184236  Cd Length: 168  Bit Score: 44.16  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481  47 HVTLSFQGSITLEDIATLEETVEKVAQSFPPFEIKLGDISYYYTdkkgSDSVIYIGIVDPEKnISALYKTLAKQLrLSGf 126
Cdd:PRK13679  34 HITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAP----TNNVIYFKVEKTEE-LEELHERLHSGD-FYG- 106

                         90
                 ....*....|....
gi 818607481 127 SPTNRIDPHITIGR 140
Cdd:PRK13679 107 EAEYAFVPHITIGQ 120
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 101-150 6.06e-04

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: 37.39  E-value: 6.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 818607481  101 IGIVDPEK-NISALYKTLAKQLRLSGFSPTNRIDPHITIGRLAKRKDRQLQ 150
Cdd:pfam02834   1 LGPPEEIAeELARLRAELERALAKLGFKPVRPFNPHITLAFLGEVDEEKLP 51
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 7-150 2.62e-03

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: 37.25  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607481    7 FIAINIP-RETKEEIGRTIENLGSKFKKYSQDLkWVDPFNLHVTLSFQGSITLEDIATLEETVEKVAQSF------PPFE 79
Cdd:pfam10469   4 FLSIPLNsPELRKRLEEFQESVLKQLPGLDESL-FIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIkdilngNPLS 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818607481   80 IKLGDISYYYTDKKGSDsVIYIGiVDPEKNISALYK---TLAKQLRLSGFSPT---NRIDPHITIGRLAKRKDRQLQ 150
Cdd:pfam10469  83 LRFKGLETFNDDPSAVR-VLYAK-VEEDDHSPKLQEladRIIRRFQEAGLLVKennSRVKLHMTLMNTRYRKKKYAK 157
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH