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Conserved domains on  [gi|2172664104|ref|NP_001386005|]
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mRNA turnover protein 4 homolog isoform 1 [Rattus norvegicus]

Protein Classification

mRNA turnover 4 family protein( domain architecture ID 10146578)

mRNA turnover 4 (MRT4) family protein is a component of the ribosome assembly machinery

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ribosomal_P0_like cd05796
Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized ...
 21-183 2.35e-105

Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.


:

Pssm-ID: 240222 [Multi-domain]  Cd Length: 163  Bit Score: 301.42  E-value: 2.35e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  21 ELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKNKVMMVALGRSPSDEYKDNLHQVSKKLRGEV 100
Cdd:cd05796     1 ELKQKLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKDSRFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 101 GLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPGPLKQFPHSMEPQLRQLGLPTALKKGVVTLLSDYEVCKEGD 180
Cdd:cd05796    81 GLLFTNEPPEEVIEYFDSYSEPDFARAGSIATETVTLPEGPLEQFPHSMEPQLRKLGLPTKLKKGVITLEADYVVCEEGK 160


                  ...
gi 2172664104 181 VLT 183
Cdd:cd05796   161 VLT 163
 
Name Accession Description Interval E-value
Ribosomal_P0_like cd05796
Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized ...
 21-183 2.35e-105

Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.


Pssm-ID: 240222 [Multi-domain]  Cd Length: 163  Bit Score: 301.42  E-value: 2.35e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  21 ELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKNKVMMVALGRSPSDEYKDNLHQVSKKLRGEV 100
Cdd:cd05796     1 ELKQKLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKDSRFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 101 GLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPGPLKQFPHSMEPQLRQLGLPTALKKGVVTLLSDYEVCKEGD 180
Cdd:cd05796    81 GLLFTNEPPEEVIEYFDSYSEPDFARAGSIATETVTLPEGPLEQFPHSMEPQLRKLGLPTKLKKGVITLEADYVVCEEGK 160


                  ...
gi 2172664104 181 VLT 183
Cdd:cd05796   161 VLT 163
RL10P_insert pfam17777
Insertion domain in 60S ribosomal protein L10P; This domain is found in prokaryotic and ...
 125-194 4.69e-33

Insertion domain in 60S ribosomal protein L10P; This domain is found in prokaryotic and archaeal ribosomal L10 protein.


Pssm-ID: 465500 [Multi-domain]  Cd Length: 71  Bit Score: 114.61  E-value: 4.69e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 125 ARAGNKATLTVSLDPGPLKQFPHSMEPQLRQLGLPTALKKGVVTLLSDYEVCKEGDVLTPEQARVLKLFG 194
Cdd:pfam17777   1 ARAGAIATEDVVLPAGPTGLAPGPIEPQLRALGIPTKIKKGKIEITKDYTVCKEGEKLTPEQANLLKLLG 70
rplP0 PRK04019
acidic ribosomal protein P0; Validated
 23-209 2.70e-23

acidic ribosomal protein P0; Validated


Pssm-ID: 179712 [Multi-domain]  Cd Length: 330  Bit Score: 95.70  E-value: 2.70e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  23 KQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIR-NAWKHSRMFFGKNKVMMVALGRSPSDEYKDnlhqVSKKLRGEVG 101
Cdd:PRK04019    8 KKEEVEELKELIKSYPVVGIVDLEGIPARQLQEIRrKLRGKAELKVSKNTLIKRALEEAGEEDLEK----LEDYLEGQVA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 102 LLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTV-------SLDPGPlkqfphsMEPQLRQLGLPTALKKGVVTLLSDYE 174
Cdd:PRK04019   84 LIFTNMNPFKLYKLLEKSKTPAPAKPGDIAPEDIvvpagptGFPPGP-------ILSELQKLGIPARIQKGKIVIKKDTV 156

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2172664104 175 VCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWD 209
Cdd:PRK04019  157 VAKAGEVISPELANVLQKLGIKPIEVGLDLKAAYE 191
 
Name Accession Description Interval E-value
Ribosomal_P0_like cd05796
Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized ...
 21-183 2.35e-105

Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.


Pssm-ID: 240222 [Multi-domain]  Cd Length: 163  Bit Score: 301.42  E-value: 2.35e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  21 ELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKNKVMMVALGRSPSDEYKDNLHQVSKKLRGEV 100
Cdd:cd05796     1 ELKQKLVENIREAVDKYKYIYVFSVDNMRNNKLKDIRQEWKDSRFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 101 GLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPGPLKQFPHSMEPQLRQLGLPTALKKGVVTLLSDYEVCKEGD 180
Cdd:cd05796    81 GLLFTNEPPEEVIEYFDSYSEPDFARAGSIATETVTLPEGPLEQFPHSMEPQLRKLGLPTKLKKGVITLEADYVVCEEGK 160


                  ...
gi 2172664104 181 VLT 183
Cdd:cd05796   161 VLT 163
Ribosomal_L10_P0 cd00379
Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in ...
 21-179 3.89e-35

Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.


Pssm-ID: 238222 [Multi-domain]  Cd Length: 155  Bit Score: 122.67  E-value: 3.89e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  21 ELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHS--RMFFGKNKVMMVALGRSPSDEYKDnlhqvskKLRG 98
Cdd:cd00379     1 EKKEELVEELKELLKKYKSVVVVDYRGLTVAQLTELRKELRESgaKLKVGKNTLMRRALKGTGFEELKP-------LLKG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  99 EVGLLFTNRTKEEVNEWFTKYT---EMDFARAGNKATLTVSldpgPLKQFPHSMEP-QLRQLGLPTALKKGVVT-LLSDY 173
Cdd:cd00379    74 PTALAFTNEDPVEVAKVLKDFAkenKKLFAKGGVVAGKVLD----PAGVTALAKLPsREELLAMLIGLLKAPIAkLARLL 149


                  ....*.
gi 2172664104 174 EVCKEG 179
Cdd:cd00379   150 NALGIG 155
RL10P_insert pfam17777
Insertion domain in 60S ribosomal protein L10P; This domain is found in prokaryotic and ...
 125-194 4.69e-33

Insertion domain in 60S ribosomal protein L10P; This domain is found in prokaryotic and archaeal ribosomal L10 protein.


Pssm-ID: 465500 [Multi-domain]  Cd Length: 71  Bit Score: 114.61  E-value: 4.69e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 125 ARAGNKATLTVSLDPGPLKQFPHSMEPQLRQLGLPTALKKGVVTLLSDYEVCKEGDVLTPEQARVLKLFG 194
Cdd:pfam17777   1 ARAGAIATEDVVLPAGPTGLAPGPIEPQLRALGIPTKIKKGKIEITKDYTVCKEGEKLTPEQANLLKLLG 70
Ribosomal_P0_L10e cd05795
Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal ...
 21-194 1.55e-25

Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.


Pssm-ID: 240221 [Multi-domain]  Cd Length: 175  Bit Score: 98.41  E-value: 1.55e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  21 ELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWK-HSRMFFGKNKVMMVALgrspsDEYKDNLHQVSK---KL 96
Cdd:cd05795     1 EWKKEYVEKLTELLKSYPKVLIVDADNVGSKQLQKIRRSLRgKAEILMGKNTLIRRAL-----RNLGDENPELEKllpYL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  97 RGEVGLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPGPLkqfphSMEP----QLRQLGLPTALKKGVVTLLSD 172
Cdd:cd05795    76 KGNVGFIFTNGDPFEIRKILEENKVPAPAKPGAIAPCDVVVPAGPT-----GMPPgptsFFQALGIPTKIEKGKIEIISD 150

                         170       180
                  ....*....|....*....|..
gi 2172664104 173 YEVCKEGDVLTPEQARVLKLFG 194
Cdd:cd05795   151 VVVVKKGEKVGASEATLLNKLN 172
rplP0 PRK04019
acidic ribosomal protein P0; Validated
 23-209 2.70e-23

acidic ribosomal protein P0; Validated


Pssm-ID: 179712 [Multi-domain]  Cd Length: 330  Bit Score: 95.70  E-value: 2.70e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  23 KQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIR-NAWKHSRMFFGKNKVMMVALGRSPSDEYKDnlhqVSKKLRGEVG 101
Cdd:PRK04019    8 KKEEVEELKELIKSYPVVGIVDLEGIPARQLQEIRrKLRGKAELKVSKNTLIKRALEEAGEEDLEK----LEDYLEGQVA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104 102 LLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTV-------SLDPGPlkqfphsMEPQLRQLGLPTALKKGVVTLLSDYE 174
Cdd:PRK04019   84 LIFTNMNPFKLYKLLEKSKTPAPAKPGDIAPEDIvvpagptGFPPGP-------ILSELQKLGIPARIQKGKIVIKKDTV 156

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2172664104 175 VCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWD 209
Cdd:PRK04019  157 VAKAGEVISPELANVLQKLGIKPIEVGLDLKAAYE 191
Ribosomal_L10 pfam00466
Ribosomal protein L10;
18-120 1.10e-19

Ribosomal protein L10;


Pssm-ID: 459822 [Multi-domain]  Cd Length: 99  Bit Score: 80.66  E-value: 1.10e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  18 KGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWK--HSRMFFGKNKVMMVALGRSPSDEykdnlhqVSKK 95
Cdd:pfam00466   1 KTREKKEELVEELKELLKEYKSVVVVDYRGLTVAQLTELRKKLRenGAELKVGKNTLMRRALEETGEEK-------LEDY 73

                          90       100
                  ....*....|....*....|....*
gi 2172664104  96 LRGEVGLLFTNRTKEEVNEWFTKYT 120
Cdd:pfam00466  74 LKGPTALLFTNEDPVAVAKVLEDFA 98
PTZ00135 PTZ00135
60S acidic ribosomal protein P0; Provisional
 14-194 1.11e-17

60S acidic ribosomal protein P0; Provisional


Pssm-ID: 240285 [Multi-domain]  Cd Length: 310  Bit Score: 80.06  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  14 KTAKKglELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWK-HSRMFFGKNKVMMVALGRSPSDeyKDNLHQV 92
Cdd:PTZ00135    3 KPEKK--AKKKAYFEKLYELLEKYKKILIVSVDNVGSKQMQDIRRSLRgKAELLMGKNTLIRKALKQRLEE--LPELEKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  93 SKKLRGEVGLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPGPLkqfphSMEPQ----LRQLGLPTALKKGVVT 168
Cdd:PTZ00135   79 LPHVKGNVGFVFTKDDLFEVKPVILENKVPAPARAGVIAPIDVVIPAGPT-----GMDPSqtsfFQALGIATKIVKGQIE 153

                         170       180
                  ....*....|....*....|....*.
gi 2172664104 169 LLSDYEVCKEGDVLTPEQARVLKLFG 194
Cdd:PTZ00135  154 ITNEVHLIKEGQKVGASQAVLLQKLN 179
PTZ00240 PTZ00240
60S ribosomal protein P0; Provisional
 21-209 3.63e-07

60S ribosomal protein P0; Provisional


Pssm-ID: 140267 [Multi-domain]  Cd Length: 323  Bit Score: 49.96  E-value: 3.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  21 ELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKhsrmffGKNKVMM------------VALGRSPSDEYKDN 88
Cdd:PTZ00240    6 TAKREYEERLVDCLTKYSCVLFVGMDNVRSQQVHDVRRALR------GKAEFVMgkktlqakivekRAQAKKASAEAKLF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2172664104  89 LHQVSKK--LRGEVGLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPGPLkqfphSMEPQ----LRQLGLPTAL 162
Cdd:PTZ00240   80 NDQCEEKnlLSGNTGLIFTNNEVQEITSVLDSHRVKAPARVGAIAPCDVIVPAGST-----GMEPTqtsfFQALNIATKI 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2172664104 163 KKGVVTLLSDYEVCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWD 209
Cdd:PTZ00240  155 AKGMVEIVTEKKVLSVGDKVDNSTATLLQKLNISPFYYQVEVLSVWD 201
 
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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