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Conserved domains on  [gi|20301988|ref|NP_620202|]
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60S ribosome subunit biogenesis protein NIP7 homolog [Rattus norvegicus]

Protein Classification

NIP7 family ribosome biogenesis protein( domain architecture ID 15340229)

NIP7 family ribosome biogenesis protein such as nucleolar pre-rRNA processing protein NIP7, which is required for proper pre-rRNA processing and ribosome subunit assembly

Gene Ontology:  GO:0003723|GO:0042255
PubMed:  36762427|20798176

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PUA_Nip7-like cd21151
PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins; The RNA-binding ...
 95-172 4.67e-56

PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. This eukaryotic and archaeal subfamily contains the conserved protein Nip7 and similar proteins, which are involved in ribosome biogenesis, taking part in 27S pre-rRNA processing and in formation of 60S ribosomal subunit. Nip7 orthologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. Structural analyses of the RNA-interacting surfaces of Saccharomyces cerevisiae and Pyrococcus abyssi Nip7 orthologs indicate that, in the archaeal PUA domain, C-terminal positively charged residues (arginines and lysines) are involved in RNA interaction while equivalent positions in eukaryotic orthologs are occupied by mostly hydrophobic residues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis.


:

Pssm-ID: 409293 [Multi-domain]  Cd Length: 78  Bit Score: 170.92  E-value: 4.67e-56
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20301988  95 YKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEY 172
Cdd:cd21151   1 YKVWLKPKAEQSFLYGNHVLKSGLGRITENTPQYQGVVVYSMNDIPLGFGVAAKSTQECRKLDPTAIVVFHQADVGEY 78
Nip7_N_euk cd21146
N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar ...
 2-88 3.82e-55

N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar proteins; This N-terminal domain of various proteins co-occurs with a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. This model contains eukaryotic Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae. Recently, it was demonstrated that human Nip7 is essential in the accurate processing of pre-rRNA. Also included is KD93, a human homolog of Nip7. Nip7 and its homologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets.


:

Pssm-ID: 409283  Cd Length: 87  Bit Score: 169.18  E-value: 3.82e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988   2 RPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHNDRVYYVSEMILKLAANISGDKLVSLGTCFGKFTKTHKFRL 81
Cdd:cd21146   1 RPLTEEETKKVFEKLAKYIGDNIKLLIDRPDGEYCFRLHKNRVYYVSEELMKLASNIPRKNLVSLGTCIGKFTKTGKFRL 80


                ....*..
gi 20301988  82 HVTALDF 88
Cdd:cd21146  81 HITALDY 87
 
Name Accession Description Interval E-value
PUA_Nip7-like cd21151
PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins; The RNA-binding ...
 95-172 4.67e-56

PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. This eukaryotic and archaeal subfamily contains the conserved protein Nip7 and similar proteins, which are involved in ribosome biogenesis, taking part in 27S pre-rRNA processing and in formation of 60S ribosomal subunit. Nip7 orthologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. Structural analyses of the RNA-interacting surfaces of Saccharomyces cerevisiae and Pyrococcus abyssi Nip7 orthologs indicate that, in the archaeal PUA domain, C-terminal positively charged residues (arginines and lysines) are involved in RNA interaction while equivalent positions in eukaryotic orthologs are occupied by mostly hydrophobic residues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis.


Pssm-ID: 409293 [Multi-domain]  Cd Length: 78  Bit Score: 170.92  E-value: 4.67e-56
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20301988  95 YKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEY 172
Cdd:cd21151   1 YKVWLKPKAEQSFLYGNHVLKSGLGRITENTPQYQGVVVYSMNDIPLGFGVAAKSTQECRKLDPTAIVVFHQADVGEY 78
Nip7_N_euk cd21146
N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar ...
 2-88 3.82e-55

N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar proteins; This N-terminal domain of various proteins co-occurs with a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. This model contains eukaryotic Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae. Recently, it was demonstrated that human Nip7 is essential in the accurate processing of pre-rRNA. Also included is KD93, a human homolog of Nip7. Nip7 and its homologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets.


Pssm-ID: 409283  Cd Length: 87  Bit Score: 169.18  E-value: 3.82e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988   2 RPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHNDRVYYVSEMILKLAANISGDKLVSLGTCFGKFTKTHKFRL 81
Cdd:cd21146   1 RPLTEEETKKVFEKLAKYIGDNIKLLIDRPDGEYCFRLHKNRVYYVSEELMKLASNIPRKNLVSLGTCIGKFTKTGKFRL 80


                ....*..
gi 20301988  82 HVTALDF 88
Cdd:cd21146  81 HITALDY 87
UPF0113_N pfam17833
UPF0113 Pre-PUA domain;
2-83 2.73e-26

UPF0113 Pre-PUA domain;


Pssm-ID: 436078  Cd Length: 77  Bit Score: 95.44  E-value: 2.73e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988     2 RPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTycfrlHNDRVYYVSEMILKLAANISGDKLVSLGTCFGKFTKTHKFRL 81
Cdd:pfam17833   1 RPLKEEEIKKVFKKLSKYIGDNVKDLLDVREGE-----ENKRVFYVSKELLKLVSKIPRKNLVSAGTCIGKFTKKKKFRL 75


                  ..
gi 20301988    82 HV 83
Cdd:pfam17833  76 SI 77
UPF0113 pfam03657
UPF0113 PUA domain;
96-175 1.32e-25

UPF0113 PUA domain;


Pssm-ID: 461006 [Multi-domain]  Cd Length: 73  Bit Score: 93.52  E-value: 1.32e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988    96 KVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCrkvdpmaIVVFHQADIGEYIRH 175
Cdd:pfam03657   1 KVWVKEKGEKLFLYGRDVLKESILKITEPVKENIVVVVLNENGEPLGFGRTRKASPGG-------KVVKNLADLGEYLRR 73
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
95-170 6.49e-19

Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 76.53  E-value: 6.49e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 20301988     95 YKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCRKVDPMAIVVFHQADIG 170
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKGKGLAVKVRRAVM 76
 
Name Accession Description Interval E-value
PUA_Nip7-like cd21151
PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins; The RNA-binding ...
 95-172 4.67e-56

PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. This eukaryotic and archaeal subfamily contains the conserved protein Nip7 and similar proteins, which are involved in ribosome biogenesis, taking part in 27S pre-rRNA processing and in formation of 60S ribosomal subunit. Nip7 orthologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. Structural analyses of the RNA-interacting surfaces of Saccharomyces cerevisiae and Pyrococcus abyssi Nip7 orthologs indicate that, in the archaeal PUA domain, C-terminal positively charged residues (arginines and lysines) are involved in RNA interaction while equivalent positions in eukaryotic orthologs are occupied by mostly hydrophobic residues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis.


Pssm-ID: 409293 [Multi-domain]  Cd Length: 78  Bit Score: 170.92  E-value: 4.67e-56
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20301988  95 YKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEY 172
Cdd:cd21151   1 YKVWLKPKAEQSFLYGNHVLKSGLGRITENTPQYQGVVVYSMNDIPLGFGVAAKSTQECRKLDPTAIVVFHQADVGEY 78
Nip7_N_euk cd21146
N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar ...
 2-88 3.82e-55

N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar proteins; This N-terminal domain of various proteins co-occurs with a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. This model contains eukaryotic Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae. Recently, it was demonstrated that human Nip7 is essential in the accurate processing of pre-rRNA. Also included is KD93, a human homolog of Nip7. Nip7 and its homologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets.


Pssm-ID: 409283  Cd Length: 87  Bit Score: 169.18  E-value: 3.82e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988   2 RPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHNDRVYYVSEMILKLAANISGDKLVSLGTCFGKFTKTHKFRL 81
Cdd:cd21146   1 RPLTEEETKKVFEKLAKYIGDNIKLLIDRPDGEYCFRLHKNRVYYVSEELMKLASNIPRKNLVSLGTCIGKFTKTGKFRL 80


                ....*..
gi 20301988  82 HVTALDF 88
Cdd:cd21146  81 HITALDY 87
Nip7_N-like cd11601
N-terminal domain of Nip7 and similar proteins; This domain of various proteins is often found ...
 2-88 7.88e-30

N-terminal domain of Nip7 and similar proteins; This domain of various proteins is often found N-terminal to a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. The family contains Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae. Recently, it was demonstrated that human Nip7 is essential in the accurate processing of pre-rRNA. Also included are KD93, a human homolog of Nip7, as well as an archaeal homolog and bacterial RsmB/RsmF family ribosomal methyltransferases.


Pssm-ID: 409282  Cd Length: 76  Bit Score: 104.60  E-value: 7.88e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988   2 RPLTEEETRVMFEKIAKYIGEnlqllvdrpdGTYCFRLHNDRVYYVSEMILKLAANISGDKlVSLGTCFGKFTKTHKFRL 81
Cdd:cd11601   1 RQ*TKEEEKLWTEFSNKYHYE----------ATGRFLVFNDHVYEVPEELAKSLDGIKVVP-YSLGTHLGDFKKDNKFEP 69


                ....*..
gi 20301988  82 HVTALDF 88
Cdd:cd11601  70 SYALALA 76
UPF0113_N pfam17833
UPF0113 Pre-PUA domain;
2-83 2.73e-26

UPF0113 Pre-PUA domain;


Pssm-ID: 436078  Cd Length: 77  Bit Score: 95.44  E-value: 2.73e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988     2 RPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTycfrlHNDRVYYVSEMILKLAANISGDKLVSLGTCFGKFTKTHKFRL 81
Cdd:pfam17833   1 RPLKEEEIKKVFKKLSKYIGDNVKDLLDVREGE-----ENKRVFYVSKELLKLVSKIPRKNLVSAGTCIGKFTKKKKFRL 75


                  ..
gi 20301988    82 HV 83
Cdd:pfam17833  76 SI 77
UPF0113 pfam03657
UPF0113 PUA domain;
96-175 1.32e-25

UPF0113 PUA domain;


Pssm-ID: 461006 [Multi-domain]  Cd Length: 73  Bit Score: 93.52  E-value: 1.32e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20301988    96 KVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCrkvdpmaIVVFHQADIGEYIRH 175
Cdd:pfam03657   1 KVWVKEKGEKLFLYGRDVLKESILKITEPVKENIVVVVLNENGEPLGFGRTRKASPGG-------KVVKNLADLGEYLRR 73
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
95-170 6.49e-19

Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 76.53  E-value: 6.49e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 20301988     95 YKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCRKVDPMAIVVFHQADIG 170
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKGKGLAVKVRRAVM 76
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 95-167 3.60e-17

PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, and a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was also found in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in regulating the expression of other genes. It has been shown that the PUA domain acts as an RNA binding domain in at least some of the proteins involved in RNA metabolism.


Pssm-ID: 409289 [Multi-domain]  Cd Length: 73  Bit Score: 71.94  E-value: 3.60e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20301988  95 YKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADVPLGFGVAAKSTQDCRKvDPMAIVVFHQA 167
Cdd:cd07953   1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSEGGRPLAIGVAEMSSDEMKE-ELKGIAVRVLH 72
 
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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