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Conserved domains on  [gi|17552478|ref|NP_498110|]
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rRNA-processing protein UTP23 homolog [Caenorhabditis elegans]

Protein Classification

rRNA-processing UTP23 family protein( domain architecture ID 10177248)

rRNA-processing UTP23 (U three protein 23) family protein, such as mammalian rRNA-processing protein UTP23 homolog that is involved in rRNA-processing and ribosome biogenesis

Gene Ontology:  GO:0070181|GO:0006364|GO:0042254
PubMed:  21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Fcf1-Utp23-H cd09866
VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in ...
 19-149 2.92e-65

VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in eukaryotes except fungi; similar to human rRNA-processing protein UTP23; PIN domain homologs of Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23, essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly, are included in this subfamily. It includes human UTP24 which hUTP24 plays a crucial role in human rRNA processing and is essential for accurate endonucleolytic cleavage at the 5'-end of 18S rRNA. Fcf1 is a component of the small subunit (SSU) processome and an essential nucleolar protein required for processing of the 18S pre-rRNA at sites A0-A2. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The Fcf1-Utp23 homolog PIN domain subfamily has three of these conserved acidic residues rather than the four seen in the Fcf1 PIN domain subfamily.


:

Pssm-ID: 350214 [Multi-domain]  Cd Length: 130  Bit Score: 198.18  E-value: 2.92e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478  19 NYKFVAPYRVLVDGTFCNAALQEKLNLAEQIPKYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAKQFEIAECTHST-PR 97
Cdd:cd09866   1 NFGFREPYQVLVDGTFCQAALKNKVNIKEQLPKYLQAEVKLCTTQCVIKELEKLGPLLYGALLILKQFQVHKCGHEKkPV 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 17552478  98 AASDCLAHLARRAAsgKTKYLIATQDDELTEKLRAIVGTPIMYIKFKTVLLD 149
Cdd:cd09866  81 SASECLKSMIKKNN--PNHYFVATQDPELQEKLRKIPGVPLLYLHNNTITLE 130
 
Name Accession Description Interval E-value
PIN_Fcf1-Utp23-H cd09866
VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in ...
 19-149 2.92e-65

VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in eukaryotes except fungi; similar to human rRNA-processing protein UTP23; PIN domain homologs of Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23, essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly, are included in this subfamily. It includes human UTP24 which hUTP24 plays a crucial role in human rRNA processing and is essential for accurate endonucleolytic cleavage at the 5'-end of 18S rRNA. Fcf1 is a component of the small subunit (SSU) processome and an essential nucleolar protein required for processing of the 18S pre-rRNA at sites A0-A2. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The Fcf1-Utp23 homolog PIN domain subfamily has three of these conserved acidic residues rather than the four seen in the Fcf1 PIN domain subfamily.


Pssm-ID: 350214 [Multi-domain]  Cd Length: 130  Bit Score: 198.18  E-value: 2.92e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478  19 NYKFVAPYRVLVDGTFCNAALQEKLNLAEQIPKYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAKQFEIAECTHST-PR 97
Cdd:cd09866   1 NFGFREPYQVLVDGTFCQAALKNKVNIKEQLPKYLQAEVKLCTTQCVIKELEKLGPLLYGALLILKQFQVHKCGHEKkPV 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 17552478  98 AASDCLAHLARRAAsgKTKYLIATQDDELTEKLRAIVGTPIMYIKFKTVLLD 149
Cdd:cd09866  81 SASECLKSMIKKNN--PNHYFVATQDPELQEKLRKIPGVPLLYLHNNTITLE 130
Fcf1 pfam04900
Fcf1; Fcf1 is a nucleolar protein involved in pre-rRNA processing. Depletion of yeast Fcf1 and ...
 51-150 9.59e-33

Fcf1; Fcf1 is a nucleolar protein involved in pre-rRNA processing. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits.


Pssm-ID: 461470  Cd Length: 99  Bit Score: 114.15  E-value: 9.59e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478    51 KYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAKQFEIAECTH-STPRAASDCLahLARRAASGKTKYLIATQDDELTEK 129
Cdd:pfam04900   1 KTLQGKVKPMITQCVIAELEKLGPKFRGALDIAKRFERRRCNHpKKPTSADDCI--VSRVGPGNKHRYIVATQDRDLRRR 78

                          90       100
                  ....*....|....*....|.
gi 17552478   130 LRAIVGTPIMYIKFKTVLLDN 150
Cdd:pfam04900  79 LRKIPGVPLLYINRSVMVLEP 99
 
Name Accession Description Interval E-value
PIN_Fcf1-Utp23-H cd09866
VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in ...
 19-149 2.92e-65

VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in eukaryotes except fungi; similar to human rRNA-processing protein UTP23; PIN domain homologs of Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23, essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly, are included in this subfamily. It includes human UTP24 which hUTP24 plays a crucial role in human rRNA processing and is essential for accurate endonucleolytic cleavage at the 5'-end of 18S rRNA. Fcf1 is a component of the small subunit (SSU) processome and an essential nucleolar protein required for processing of the 18S pre-rRNA at sites A0-A2. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The Fcf1-Utp23 homolog PIN domain subfamily has three of these conserved acidic residues rather than the four seen in the Fcf1 PIN domain subfamily.


Pssm-ID: 350214 [Multi-domain]  Cd Length: 130  Bit Score: 198.18  E-value: 2.92e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478  19 NYKFVAPYRVLVDGTFCNAALQEKLNLAEQIPKYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAKQFEIAECTHST-PR 97
Cdd:cd09866   1 NFGFREPYQVLVDGTFCQAALKNKVNIKEQLPKYLQAEVKLCTTQCVIKELEKLGPLLYGALLILKQFQVHKCGHEKkPV 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 17552478  98 AASDCLAHLARRAAsgKTKYLIATQDDELTEKLRAIVGTPIMYIKFKTVLLD 149
Cdd:cd09866  81 SASECLKSMIKKNN--PNHYFVATQDPELQEKLRKIPGVPLLYLHNNTITLE 130
PIN_Fcf1-like cd08553
VapC-like PIN domain of rRNA-processing proteins, Fcf1 (Utp24, YDR339C), Utp23 (YOR004W), and ...
 26-149 5.89e-37

VapC-like PIN domain of rRNA-processing proteins, Fcf1 (Utp24, YDR339C), Utp23 (YOR004W), and other eukaryotic homologs; Fcf1 (FAF1-copurifying factor 1, also known as Utp24) and Utp23 (U three-associated protein 23) are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly. Components of the small subunit (SSU) processome, Fcf1 and Utp23 are essential nucleolar proteins that are required for processing of the 18S pre-rRNA at sites A0-A2. The Fcf1 protein was reported to interact with Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of the ubiquinol-cytochrome c reductase complex). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. The subfamily of Fcf1- and Utp23-like homologs have three of the four conserved residues found in S. cerevisiae Fcf1. Some members of the superfamily, including S. cerevisiae Utp23, lack several of these key catalytic residues. Mutation of the remaining conserved putative active site residues seen in Utp23 did not interfere with rRNA maturation and cell viability. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350202 [Multi-domain]  Cd Length: 123  Bit Score: 125.77  E-value: 5.89e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478  26 YRVLVDGTFCNAALQEKLNLAEQIPKYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAKQFEIAECTHSTPR-AASDCLA 104
Cdd:cd08553   1 YQVLVDGNFIHAALQKKIDLKEALPKLLGGKVKLFVTRCVLAELRSLGEDFSGALLAAKRFERRRCNHEEGPvSAAECIL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 17552478 105 HLARraASGKTKYLIATQDDELTEKLRAIVGTPIMYIKFKTVLLD 149
Cdd:cd08553  81 DIIG--KNNEEHYFVATQDTELRKKLRKIPGVPLLYINRNVLILE 123
Fcf1 pfam04900
Fcf1; Fcf1 is a nucleolar protein involved in pre-rRNA processing. Depletion of yeast Fcf1 and ...
 51-150 9.59e-33

Fcf1; Fcf1 is a nucleolar protein involved in pre-rRNA processing. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits.


Pssm-ID: 461470  Cd Length: 99  Bit Score: 114.15  E-value: 9.59e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478    51 KYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAKQFEIAECTH-STPRAASDCLahLARRAASGKTKYLIATQDDELTEK 129
Cdd:pfam04900   1 KTLQGKVKPMITQCVIAELEKLGPKFRGALDIAKRFERRRCNHpKKPTSADDCI--VSRVGPGNKHRYIVATQDRDLRRR 78

                          90       100
                  ....*....|....*....|.
gi 17552478   130 LRAIVGTPIMYIKFKTVLLDN 150
Cdd:pfam04900  79 LRKIPGVPLLYINRSVMVLEP 99
PIN_ScUtp23p-like cd09865
VapC-like PIN domain of rRNA-processing protein, Utp23 (YOR004W), and other fungal homologs; ...
 4-148 1.10e-25

VapC-like PIN domain of rRNA-processing protein, Utp23 (YOR004W), and other fungal homologs; Saccharomyces cerevisiae Utp23 (U three-associated protein 23), component of the small subunit (SSU) processome, is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily, including S. cerevisiae Utp23, lack several of these key catalytic residues. Mutation of the remaining conserved putative active site residues seen in Utp23 did not interfere with rRNA maturation and cell viability. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350213 [Multi-domain]  Cd Length: 149  Bit Score: 97.68  E-value: 1.10e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478   4 KRLKRANRLLTFYKYNYKFVAPYRVLVDGTFCNAALQEKLNLAEQIPKYLTEETHLMTTNCVLKELEKFGPLLYGAFVIA 83
Cdd:cd09865   2 KRAKAYRKLMHVYQLTFGFREPYQVLVDDDFLLEAAKQKMDLLKRLERVLQGEVKPMITQCCIQALYALGPKNQPAIDLA 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17552478  84 KQFEIAECTHS-TPRAASDCLAHLARRAASGKTKYLIATQDDELTEKLRAIVGTPIMYIKfKTVLL 148
Cdd:cd09865  82 KTFERRRCNHReADLSPEECIKSVVGPTNKNKHRYIVATQDPKLRRKLRSVPGVPLIHIN-RSVMV 146
PIN_Fcf1-like cd09864
VapC-like PIN domain of rRNA-processing protein, Fcf1 (Utp24, YDR339C), and other eukaryotic ...
 16-142 1.67e-18

VapC-like PIN domain of rRNA-processing protein, Fcf1 (Utp24, YDR339C), and other eukaryotic homologs; Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Component of the small subunit (SSU) processome, Fcf1 is an essential nucleolar protein that is required for processing of the 18S pre-rRNA at sites A0-A2. The Fcf1 protein was reported to interact with Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of the ubiquinol-cytochrome c reductase complex). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. Most members of the Fcf1 PIN domain subfamily have four of these conserved residues and the Fcf1-Utp23 homolog PIN domain subfamily has three. Point mutation studies of the conserved acidic residues in the putative active site of Saccharomyces cerevisiae Fcf1 determined they were essential for pre-rRNA processing at sites A1 and A2, whereas the presence of the Fcf1 protein itself is also required for cleavage at site A0.


Pssm-ID: 350212  Cd Length: 131  Bit Score: 78.35  E-value: 1.67e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478  16 YKYNYKFVAPYRVLVDGTFCNAALQEKLNLAEQIPKYLTEETHLMTTNCVLKELEKFGPLLYGAFVIAK--QFEIAECTH 93
Cdd:cd09864   1 FKYNTALGPPYHVLLDTNFINFSIQNKLDIVKGMMDCLYAKCIPCITDCVMAELEKLGRKYRVALRIAKdpRFERLKCDH 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 17552478  94 STPRAAsDClahLARRAASGKTkYLIATQDDELTEKLRAIVGTPIMYIK 142
Cdd:cd09864  81 KGTYAD-DC---IVNRVTQHRC-YIVATCDRDLKRRIRKIPGVPIMYIK 124
PIN_VapC_AF0591-like cd09879
VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal ...
 40-144 4.21e-03

VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal homologs; PIN (PilT N terminus) domain of Archaeoglobus fulgidus AF0591 protein and other similar uncharacterized archaeal homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these highly conserved putative metal-binding, active site residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains and included distant subgroups, this subgroup includes some sequences belonging to one of these, PIN_14.


Pssm-ID: 350227 [Multi-domain]  Cd Length: 118  Bit Score: 35.90  E-value: 4.21e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552478  40 QEKLNLAEQIpKYLTEETHLMTTNCVLKELEKFGPLLYG--------AFVIAKQFEIAECTHSTpraASDCLAHLARraa 111
Cdd:cd09879  13 QFGVDIFEEL-ERLLGKYEIVVPSAVIEELERLAKKGKGkdkraarlALKLAERCKVVESEGEP---ADDAILELAK--- 85

                        90       100       110
                ....*....|....*....|....*....|...
gi 17552478 112 sgKTKYLIATQDDELTEKLRAIvGTPIMYIKFK 144
Cdd:cd09879  86 --ELGAIVATNDRELRKRLREK-GIPVIYLRQK 115
 
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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