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Conserved domains on  [gi|2466830421|ref|XP_054485507|]
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RNA-binding protein PNO1 [Agelaius phoeniceus]

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 ...
 143-238 1.27e-72

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: 215.91  E-value: 1.27e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 143 RLDDLFLESFEVTDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSP 222
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTKIHILGSFQNIRVARDAICSLILGSP 80

                          90
                  ....*....|....*.
gi 2466830421 223 PSKVYGNIRAVASRAA 238
Cdd:cd22392    81 PGKVYGKLRAVASRLK 96
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 63-141 7.50e-56

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: 173.10  E-value: 7.50e-56
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2466830421  63 ELRKIPVPANRYTPLKENWMKIFTPIVEHLQLQIRFNLKTRNVEIKTCQETKDLSALTKAADFVKAFILGFQVEDALAL 141
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 ...
 143-238 1.27e-72

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: 215.91  E-value: 1.27e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 143 RLDDLFLESFEVTDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSP 222
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTKIHILGSFQNIRVARDAICSLILGSP 80

                          90
                  ....*....|....*.
gi 2466830421 223 PSKVYGNIRAVASRAA 238
Cdd:cd22392    81 PGKVYGKLRAVASRLK 96
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 63-141 7.50e-56

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: 173.10  E-value: 7.50e-56
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2466830421  63 ELRKIPVPANRYTPLKENWMKIFTPIVEHLQLQIRFNLKTRNVEIKTCQETKDLSALTKAADFVKAFILGFQVEDALAL 141
Cdd:cd22391     2 EFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 88-227 2.26e-24

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 95.32  E-value: 2.26e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421  88 IVEHLQLQIRFNLKTRNVEIkTCQETKDLSALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 167
Cdd:PRK13763   28 IEERTGVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-DDYVLEVIDLSDYGDSP-NALRR 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 168 AIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSPPSKVY 227
Cdd:PRK13763  105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHGTVY 164
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 88-227 3.60e-24

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: 94.55  E-value: 3.60e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421  88 IVEHLQLQIRFNLKTRNVEIKTCQETKDlsALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 167
Cdd:TIGR03665  23 IEERTGVKLDIDSETGEVKIEPEDEDPL--AVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVIDLKEYGKSP-NALRR 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 168 AIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSPPSKVY 227
Cdd:TIGR03665  99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVY 158
KH smart00322
K homology RNA-binding domain;
166-218 7.70e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 39.97  E-value: 7.70e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2466830421  166 SRAIGRIAGKGGKTKFTIENVTRTRIVL-----ADTKIHILGSFQNIKMARTAICNLI 218
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIpgpgsEERVVEITGPPENVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 166-214 2.20e-03

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 35.72  E-value: 2.20e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2466830421 166 SRAIGRIAGKGGKTKFTIENVTRTRIVL-------ADTKIHILGSFQNIKMARTAI 214
Cdd:pfam00013   8 SSLVGLIIGKGGSNIKEIREETGAKIQIppsesegNERIVTITGTPEAVEAAKALI 63
 
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 ...
 143-238 1.27e-72

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: 215.91  E-value: 1.27e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 143 RLDDLFLESFEVTDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSP 222
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTKIHILGSFQNIRVARDAICSLILGSP 80

                          90
                  ....*....|....*.
gi 2466830421 223 PSKVYGNIRAVASRAA 238
Cdd:cd22392    81 PGKVYGKLRAVASRLK 96
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 63-141 7.50e-56

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: 173.10  E-value: 7.50e-56
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2466830421  63 ELRKIPVPANRYTPLKENWMKIFTPIVEHLQLQIRFNLKTRNVEIKTCQETKDLSALTKAADFVKAFILGFQVEDALAL 141
Cdd:cd22391     2 EFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 88-227 2.26e-24

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 95.32  E-value: 2.26e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421  88 IVEHLQLQIRFNLKTRNVEIkTCQETKDLSALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 167
Cdd:PRK13763   28 IEERTGVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-DDYVLEVIDLSDYGDSP-NALRR 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 168 AIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSPPSKVY 227
Cdd:PRK13763  105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHGTVY 164
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 88-227 3.60e-24

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: 94.55  E-value: 3.60e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421  88 IVEHLQLQIRFNLKTRNVEIKTCQETKDlsALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 167
Cdd:TIGR03665  23 IEERTGVKLDIDSETGEVKIEPEDEDPL--AVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVIDLKEYGKSP-NALRR 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2466830421 168 AIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSPPSKVY 227
Cdd:TIGR03665  99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTVY 158
KH-I_Dim2p_like_rpt2 cd22390
second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 152-227 6.73e-12

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: 59.93  E-value: 6.73e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2466830421 152 FEVTDVKPLKGD---HLSRAIGRIAGKGGKTKFTIENVTRTRIVLADTKIHILGSFQNIKMARTAICNLILGSPPSKVY 227
Cdd:cd22390    10 LEVIDLRDYAGRskkALRRVKGRVIGSGGKTRRLIEELTGCYISVYGKTVSIIGDFENLQIAKEAIEMLLNGSPHSSVY 88
KH smart00322
K homology RNA-binding domain;
166-218 7.70e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 39.97  E-value: 7.70e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2466830421  166 SRAIGRIAGKGGKTKFTIENVTRTRIVL-----ADTKIHILGSFQNIKMARTAICNLI 218
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIpgpgsEERVVEITGPPENVEKAAELILEIL 68
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 166-214 1.15e-04

fourth 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 fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 39.15  E-value: 1.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2466830421 166 SRAIGRIAGKGGKTKFTIENVTRTRIVLAD---------TKIHILGSFQNIKMARTAI 214
Cdd:cd22403     8 SSMVGRIIGKGGQNVRELQRLTGAIIKLPRdqtpdegdeVPVEIIGNFYATQSAQRRI 65
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 166-214 1.36e-04

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 38.82  E-value: 1.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2466830421 166 SRAIGRIAGKGGKTKFTIENVTRTRIVL-------ADTKIHILGSFQNIKMARTAI 214
Cdd:cd00105     7 SELVGLIIGKGGSTIKEIEEETGARIQIpkegegsGERVVTITGTPEAVEKAKELI 62
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 166-214 2.20e-03

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 35.72  E-value: 2.20e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2466830421 166 SRAIGRIAGKGGKTKFTIENVTRTRIVL-------ADTKIHILGSFQNIKMARTAI 214
Cdd:pfam00013   8 SSLVGLIIGKGGSNIKEIREETGAKIQIppsesegNERIVTITGTPEAVEAAKALI 63
 
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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