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Conserved domains on  [gi|6319791|ref|NP_009872|]
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ribosome biosynthesis protein KRR1 [Saccharomyces cerevisiae S288C]

Protein Classification

KRR1 small subunit processome component( domain architecture ID 16910090)

KRR1 small subunit (SSU) processome component is involved in the assembly of the SSU processome; contains two K-homology (KH) RNA-binding domains, the first one is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor

CATH:  3.30.1370.10
Gene Ontology:  GO:0003723|GO:0032040|GO:0042274|GO:0006364
PubMed:  11160884|18422648
SCOP:  4001190

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 121-213 3.94e-68

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


:

Pssm-ID: 411822  Cd Length: 93  Bit Score: 207.42  E-value: 3.94e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791  121 MACDVIKIGNFVTNKERFVKRRQRLVGPNGNTLKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVEDCMKNIHPIYHI 200
Cdd:cd22394   1 VACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKAIELLTKCYILVQGNTVSAIGPYKGLKEVRKIVEDCMKNIHPIYNI 80

                        90
                ....*....|...
gi 6319791  201 KELMIKRELAKRP 213
Cdd:cd22394  81 KTLMIKRELEKDP 93
KH-I_KRR1_rpt1 cd22393
first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 35-117 6.20e-51

first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 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 and is involved in binding another assembly factor, Kri1.


:

Pssm-ID: 411821  Cd Length: 83  Bit Score: 163.09  E-value: 6.20e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791   35 FAEESSFMTLFPKYRESYLKTIWNDVTRALDKHNIACVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAV 114
Cdd:cd22393   1 FLEESSFATLFPKYREKYLKEVWPLVTKALKEHGIKCELDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAV 80


                ...
gi 6319791  115 KIL 117
Cdd:cd22393  81 KIL 83
 
Name Accession Description Interval E-value
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 121-213 3.94e-68

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411822  Cd Length: 93  Bit Score: 207.42  E-value: 3.94e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791  121 MACDVIKIGNFVTNKERFVKRRQRLVGPNGNTLKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVEDCMKNIHPIYHI 200
Cdd:cd22394   1 VACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKAIELLTKCYILVQGNTVSAIGPYKGLKEVRKIVEDCMKNIHPIYNI 80

                        90
                ....*....|...
gi 6319791  201 KELMIKRELAKRP 213
Cdd:cd22394  81 KTLMIKRELEKDP 93
KH-I_KRR1_rpt1 cd22393
first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 35-117 6.20e-51

first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 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 and is involved in binding another assembly factor, Kri1.


Pssm-ID: 411821  Cd Length: 83  Bit Score: 163.09  E-value: 6.20e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791   35 FAEESSFMTLFPKYRESYLKTIWNDVTRALDKHNIACVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAV 114
Cdd:cd22393   1 FLEESSFATLFPKYREKYLKEVWPLVTKALKEHGIKCELDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAV 80


                ...
gi 6319791  115 KIL 117
Cdd:cd22393  81 KIL 83
KH_8 pfam17903
Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ...
 39-119 1.40e-29

Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1.


Pssm-ID: 407755  Cd Length: 81  Bit Score: 107.83  E-value: 1.40e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791     39 SSFMTLFPKYRESYLKTIWNDVTRALDKHNIACVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAVKILQ 118
Cdd:pfam17903   1 SSFEILFPKHREQYLKGVEEYIRELLEEKKIKCEVDYDERSIKVSTTEKTRDPYVILKARDFIKLVSRGVPLEEAVKVFE 80


                  .
gi 6319791    119 D 119
Cdd:pfam17903  81 D 81
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 71-188 1.22e-13

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: 67.97  E-value: 1.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791     71 CVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAVKILQDDMACDVIKIGNFVTNKERFVKRRQRLVGPNG 150
Cdd:TIGR03665  29 VKLDIDSETGEVKIEPEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGG 108

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 6319791    151 NTLKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVE 188
Cdd:TIGR03665 109 KTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIE 146
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 73-188 3.43e-12

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 63.73  E-value: 3.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791    73 LDLVEGSMTVKTTrKTYDPAIILKARDLIKLLARSVPFPQAVKILQDDMACDVIKIGNFVTNKERFVKRRQRLVGPNGNT 152
Cdd:PRK13763  38 IDSETGEVIIEPT-DGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKT 116

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 6319791   153 LKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVE 188
Cdd:PRK13763 117 RRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIE 152
KH smart00322
K homology RNA-binding domain;
139-191 1.37e-03

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 36.50  E-value: 1.37e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 6319791     139 VKRRQRLVGPNGNTLKALELLTKCYILVQG-----NTVSAMGPFKGLKEVRRVVEDCM 191
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIPGpgseeRVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 121-213 3.94e-68

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411822  Cd Length: 93  Bit Score: 207.42  E-value: 3.94e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791  121 MACDVIKIGNFVTNKERFVKRRQRLVGPNGNTLKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVEDCMKNIHPIYHI 200
Cdd:cd22394   1 VACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKAIELLTKCYILVQGNTVSAIGPYKGLKEVRKIVEDCMKNIHPIYNI 80

                        90
                ....*....|...
gi 6319791  201 KELMIKRELAKRP 213
Cdd:cd22394  81 KTLMIKRELEKDP 93
KH-I_KRR1_rpt1 cd22393
first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 35-117 6.20e-51

first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 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 and is involved in binding another assembly factor, Kri1.


Pssm-ID: 411821  Cd Length: 83  Bit Score: 163.09  E-value: 6.20e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791   35 FAEESSFMTLFPKYRESYLKTIWNDVTRALDKHNIACVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAV 114
Cdd:cd22393   1 FLEESSFATLFPKYREKYLKEVWPLVTKALKEHGIKCELDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAV 80


                ...
gi 6319791  115 KIL 117
Cdd:cd22393  81 KIL 83
KH_8 pfam17903
Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ...
 39-119 1.40e-29

Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1.


Pssm-ID: 407755  Cd Length: 81  Bit Score: 107.83  E-value: 1.40e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791     39 SSFMTLFPKYRESYLKTIWNDVTRALDKHNIACVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAVKILQ 118
Cdd:pfam17903   1 SSFEILFPKHREQYLKGVEEYIRELLEEKKIKCEVDYDERSIKVSTTEKTRDPYVILKARDFIKLVSRGVPLEEAVKVFE 80


                  .
gi 6319791    119 D 119
Cdd:pfam17903  81 D 81
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 71-188 1.22e-13

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: 67.97  E-value: 1.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791     71 CVLDLVEGSMTVKTTRKTYDPAIILKARDLIKLLARSVPFPQAVKILQDDMACDVIKIGNFVTNKERFVKRRQRLVGPNG 150
Cdd:TIGR03665  29 VKLDIDSETGEVKIEPEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGG 108

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 6319791    151 NTLKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVE 188
Cdd:TIGR03665 109 KTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIE 146
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 73-188 3.43e-12

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 63.73  E-value: 3.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319791    73 LDLVEGSMTVKTTrKTYDPAIILKARDLIKLLARSVPFPQAVKILQDDMACDVIKIGNFVTNKERFVKRRQRLVGPNGNT 152
Cdd:PRK13763  38 IDSETGEVIIEPT-DGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKT 116

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 6319791   153 LKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVE 188
Cdd:PRK13763 117 RRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIE 152
KH-I_Dim2p_like_rpt2 cd22390
second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 115-188 4.33e-10

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: 55.69  E-value: 4.33e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6319791  115 KILQDDMACDVIKIGNFVTNKERFVKR-RQRLVGPNGNTLKALELLTKCYILVQGNTVSAMGPFKGLKEVRRVVE 188
Cdd:cd22390   2 LLLDDDYVLEVIDLRDYAGRSKKALRRvKGRVIGSGGKTRRLIEELTGCYISVYGKTVSIIGDFENLQIAKEAIE 76
KH smart00322
K homology RNA-binding domain;
139-191 1.37e-03

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 36.50  E-value: 1.37e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 6319791     139 VKRRQRLVGPNGNTLKALELLTKCYILVQG-----NTVSAMGPFKGLKEVRRVVEDCM 191
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIPGpgseeRVVEITGPPENVEKAAELILEIL 68
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 144-168 9.27e-03

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411811 [Multi-domain]  Cd Length: 101  Bit Score: 35.02  E-value: 9.27e-03
                        10        20
                ....*....|....*....|....*
gi 6319791  144 RLVGPNGNTLKALELLTKCYILVQG 168
Cdd:cd22383  21 RILGPRGMTAKQLEQDTGCKIMIRG 45
 
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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