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Conserved domains on  [gi|17537417|ref|NP_496099|]
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RNA-binding protein pno-1 [Caenorhabditis elegans]

Protein Classification

pre-rRNA-processing protein PNO1( domain architecture ID 16910075)

pre-rRNA-processing protein PNO1 is required for small ribosomal subunit (SSU) synthesis and has a role in the processing of early nucleolar and late cytoplasmic pre-RNA species

CATH:  3.30.1370.10
Gene Ontology:  GO:0003723|GO:0042254
PubMed:  18422648|11160884
SCOP:  4001190

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 178-274 1.30e-57

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


:

Pssm-ID: 411820  Cd Length: 96  Bit Score: 179.32  E-value: 1.30e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417 178 RLDHLFLETFEVADVKHsLKGDHVSRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGS 257
Cdd:cd22392   1 RLDDLYIESFEVKDVKT-LKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTKIHILGSFQNIRVARDAICSLILGS 79

                        90
                ....*....|....*..
gi 17537417 258 NPSKVYGSLRNMASRGA 274
Cdd:cd22392  80 PPGKVYGKLRAVASRLK 96
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 98-176 9.30e-46

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411819  Cd Length: 80  Bit Score: 148.45  E-value: 9.30e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17537417  98 ESRVVPVPKHRYTPLKDNWVNIFTPIVKNLGLQVRFNLKKRQVEIRNPVDREDTTDLQKATDFVRAFILGFEVNDAIAL 176
Cdd:cd22391   2 EFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
 
Name Accession Description Interval E-value
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 178-274 1.30e-57

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411820  Cd Length: 96  Bit Score: 179.32  E-value: 1.30e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417 178 RLDHLFLETFEVADVKHsLKGDHVSRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGS 257
Cdd:cd22392   1 RLDDLYIESFEVKDVKT-LKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTKIHILGSFQNIRVARDAICSLILGS 79

                        90
                ....*....|....*..
gi 17537417 258 NPSKVYGSLRNMASRGA 274
Cdd:cd22392  80 PPGKVYGKLRAVASRLK 96
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 98-176 9.30e-46

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411819  Cd Length: 80  Bit Score: 148.45  E-value: 9.30e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17537417  98 ESRVVPVPKHRYTPLKDNWVNIFTPIVKNLGLQVRFNLKKRQVEIRNPVDREDTTDLQKATDFVRAFILGFEVNDAIAL 176
Cdd:cd22391   2 EFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 102-266 1.42e-18

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 81.07  E-value: 1.42e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417  102 VPVPKHRYTPLKDNWVNIFTPIVKNLGLQVRFNLKKRQVEIRnPVDREDTTDLQKATDFVRAFILGFEVNDAIALIRLDh 181
Cdd:PRK13763   7 VKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIE-PTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDD- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417  182 lflETFEVADVK-HSLKGDHVSRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGSNPS 260
Cdd:PRK13763  85 ---YVLEVIDLSdYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHG 161


                 ....*.
gi 17537417  261 KVYGSL 266
Cdd:PRK13763 162 TVYKFL 167
Krr1 COG1094
rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and ...
 149-263 5.30e-17

rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440711 [Multi-domain]  Cd Length: 177  Bit Score: 76.40  E-value: 5.30e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417 149 EDTTDLQKATDFVRAFILGFEVNDAIALIRLDhlflETFEVADVKHSLKGD-HVSRAIGRIAGKDGRTKLVIENTTKTRI 227
Cdd:COG1094  48 EDPLAALKARDIVKAIGRGFSPEKALRLLDDD----YMLEVIDLPDVGKSPnALDRIKGRIIGREGRTRRIIEELTGVDI 123

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 17537417 228 VVANTKIHILGAYQNLKLARNAVCSLILGSNPSKVY 263
Cdd:COG1094 124 SIYGKTVAIIGDFDQVEIAREAIEMLIDGRIHPTVY 159
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 123-266 3.15e-16

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 74.52  E-value: 3.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417   123 IVKNLGLQVRFNLKKRQVEIRNPVdrEDTTDLQKATDFVRAFILGFEVNDAIALIRLDhlflETFEVADVKHSLKGD-HV 201
Cdd:TIGR03665  23 IEERTGVKLDIDSETGEVKIEPED--EDPLAVMKAREVVKAIGRGFSPEKALKLLDDD----YMLEVIDLKEYGKSPnAL 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17537417   202 SRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGSNPSKVYGSL 266
Cdd:TIGR03665  97 RRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVYKFL 161
KH smart00322
K homology RNA-binding domain;
202-254 6.89e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 6.89e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17537417    202 SRAIGRIAGKDGRTKLVIENTTKTRIVV-----ANTKIHILGAYQNLKLARNAVCSLI 254
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIpgpgsEERVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 178-274 1.30e-57

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411820  Cd Length: 96  Bit Score: 179.32  E-value: 1.30e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417 178 RLDHLFLETFEVADVKHsLKGDHVSRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGS 257
Cdd:cd22392   1 RLDDLYIESFEVKDVKT-LKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTKIHILGSFQNIRVARDAICSLILGS 79

                        90
                ....*....|....*..
gi 17537417 258 NPSKVYGSLRNMASRGA 274
Cdd:cd22392  80 PPGKVYGKLRAVASRLK 96
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 98-176 9.30e-46

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411819  Cd Length: 80  Bit Score: 148.45  E-value: 9.30e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17537417  98 ESRVVPVPKHRYTPLKDNWVNIFTPIVKNLGLQVRFNLKKRQVEIRNPVDREDTTDLQKATDFVRAFILGFEVNDAIAL 176
Cdd:cd22391   2 EFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 102-266 1.42e-18

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 81.07  E-value: 1.42e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417  102 VPVPKHRYTPLKDNWVNIFTPIVKNLGLQVRFNLKKRQVEIRnPVDREDTTDLQKATDFVRAFILGFEVNDAIALIRLDh 181
Cdd:PRK13763   7 VKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIE-PTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDD- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417  182 lflETFEVADVK-HSLKGDHVSRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGSNPS 260
Cdd:PRK13763  85 ---YVLEVIDLSdYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHG 161


                 ....*.
gi 17537417  261 KVYGSL 266
Cdd:PRK13763 162 TVYKFL 167
Krr1 COG1094
rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and ...
 149-263 5.30e-17

rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440711 [Multi-domain]  Cd Length: 177  Bit Score: 76.40  E-value: 5.30e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417 149 EDTTDLQKATDFVRAFILGFEVNDAIALIRLDhlflETFEVADVKHSLKGD-HVSRAIGRIAGKDGRTKLVIENTTKTRI 227
Cdd:COG1094  48 EDPLAALKARDIVKAIGRGFSPEKALRLLDDD----YMLEVIDLPDVGKSPnALDRIKGRIIGREGRTRRIIEELTGVDI 123

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 17537417 228 VVANTKIHILGAYQNLKLARNAVCSLILGSNPSKVY 263
Cdd:COG1094 124 SIYGKTVAIIGDFDQVEIAREAIEMLIDGRIHPTVY 159
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 123-266 3.15e-16

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 74.52  E-value: 3.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17537417   123 IVKNLGLQVRFNLKKRQVEIRNPVdrEDTTDLQKATDFVRAFILGFEVNDAIALIRLDhlflETFEVADVKHSLKGD-HV 201
Cdd:TIGR03665  23 IEERTGVKLDIDSETGEVKIEPED--EDPLAVMKAREVVKAIGRGFSPEKALKLLDDD----YMLEVIDLKEYGKSPnAL 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17537417   202 SRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGSNPSKVYGSL 266
Cdd:TIGR03665  97 RRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVYKFL 161
KH-I_Dim2p_like_rpt2 cd22390
second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 200-268 1.46e-08

second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411818  Cd Length: 96  Bit Score: 51.07  E-value: 1.46e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17537417 200 HVSRAIGRIAGKDGRTKLVIENTTKTRIVVANTKIHILGAYQNLKLARNAVCSLILGSNPSKVYGSLRN 268
Cdd:cd22390  25 ALRRVKGRVIGSGGKTRRLIEELTGCYISVYGKTVSIIGDFENLQIAKEAIEMLLNGSPHSSVYRFLEK 93
KH smart00322
K homology RNA-binding domain;
202-254 6.89e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 6.89e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17537417    202 SRAIGRIAGKDGRTKLVIENTTKTRIVV-----ANTKIHILGAYQNLKLARNAVCSLI 254
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIpgpgsEERVVEITGPPENVEKAAELILEIL 68
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 205-231 9.82e-03

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 34.12  E-value: 9.82e-03
                        10        20
                ....*....|....*....|....*..
gi 17537417 205 IGRIAGKDGRTKLVIENTTKTRIVVAN 231
Cdd:cd22401  11 CGRLIGKDGRNIKKIMEDTNTKITISS 37
 
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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