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Conserved domains on  [gi|1379640789|ref|XP_024640382|]
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small nuclear ribonucleoprotein Sm D2 isoform X1 [Medicago truncatula]

Protein Classification

small nuclear ribonucleoprotein Sm D2( domain architecture ID 10109559)

small nuclear ribonucleoprotein Sm D2 plays role in pre-mRNA splicing as a core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as a component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome

CATH:  2.30.30.100
Gene Ontology:  GO:0030532|GO:0008380|GO:0000398|GO:0003723|GO:0000387
PubMed:  18687770|7744013|11259661

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_D2 cd01720
Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 13-102 9.91e-59

Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits.


:

Pssm-ID: 212467  Cd Length: 89  Bit Score: 174.83  E-value: 9.91e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379640789  13 FNIGPLSVLYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEVPKTGKGkKKAQPVNKDRFISKMFLRG 92
Cdd:cd01720     1 FNTGPLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKG-KKSKPVNKDRFISKMFLRG 79

                          90
                  ....*....|
gi 1379640789  93 DSVIIVLRNP 102
Cdd:cd01720    80 DSVILVLRNP 89
 
Name Accession Description Interval E-value
Sm_D2 cd01720
Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 13-102 9.91e-59

Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits.


Pssm-ID: 212467  Cd Length: 89  Bit Score: 174.83  E-value: 9.91e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379640789  13 FNIGPLSVLYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEVPKTGKGkKKAQPVNKDRFISKMFLRG 92
Cdd:cd01720     1 FNTGPLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKG-KKSKPVNKDRFISKMFLRG 79

                          90
                  ....*....|
gi 1379640789  93 DSVIIVLRNP 102
Cdd:cd01720    80 DSVILVLRNP 89
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 21-98 2.09e-13

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 59.43  E-value: 2.09e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1379640789   21 LYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEvpktgkgkkkaqpVNKDRFISKMFLRGDSVIIV 98
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------------GEKKRKLGLVFIRGNNIVYI 65
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 21-98 1.62e-12

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 57.13  E-value: 1.62e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1379640789  21 LYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEvpktgkgkkkaqpvNKDRFISKMFLRGDSVIIV 98
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD--------------GEVRKLGLVLIRGNNIVLI 64
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 17-98 2.47e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 36.52  E-value: 2.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379640789  17 PLSVLYMSVrnNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMwtevpKTGKGKKKaqpvnkdrfISKMFLRGDSVI 96
Cdd:PRK00737    5 PLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGEVVRK---------LGKVVIRGDNVV 68


                  ..
gi 1379640789  97 IV 98
Cdd:PRK00737   69 YV 70
 
Name Accession Description Interval E-value
Sm_D2 cd01720
Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 13-102 9.91e-59

Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits.


Pssm-ID: 212467  Cd Length: 89  Bit Score: 174.83  E-value: 9.91e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379640789  13 FNIGPLSVLYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEVPKTGKGkKKAQPVNKDRFISKMFLRG 92
Cdd:cd01720     1 FNTGPLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKG-KKSKPVNKDRFISKMFLRG 79

                          90
                  ....*....|
gi 1379640789  93 DSVIIVLRNP 102
Cdd:cd01720    80 DSVILVLRNP 89
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 30-98 5.53e-16

Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212477  Cd Length: 82  Bit Score: 66.48  E-value: 5.53e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1379640789  30 QVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEVPKTGKGKKKAQPVNKdRFISKMFLRGDSVIIV 98
Cdd:cd01730    13 RVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTK-RNIPMLFVRGDGVILV 80
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 21-98 2.09e-13

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 59.43  E-value: 2.09e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1379640789   21 LYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEvpktgkgkkkaqpVNKDRFISKMFLRGDSVIIV 98
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------------GEKKRKLGLVFIRGNNIVYI 65
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 21-98 1.62e-12

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 57.13  E-value: 1.62e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1379640789  21 LYMSVRNNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEvpktgkgkkkaqpvNKDRFISKMFLRGDSVIIV 98
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD--------------GEVRKLGLVLIRGNNIVLI 64
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 28-96 1.31e-07

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212462 [Multi-domain]  Cd Length: 63  Bit Score: 44.55  E-value: 1.31e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1379640789  28 NTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMWTEVpktgkgkkkaqpvnKDRFISKMFLRGDSVI 96
Cdd:cd00600     6 GKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDG--------------KVRVLGLVLIRGSNIV 60
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 17-98 2.11e-07

archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain.


Pssm-ID: 212478  Cd Length: 69  Bit Score: 44.10  E-value: 2.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379640789  17 PLSVLYMSVrnNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVrEMWTEvpktGKGKKKaqpvnkdrfISKMFLRGDSVI 96
Cdd:cd01731     2 PLDVLNESL--NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENA-EEIIE----GESVRK---------LGTVLVRGDNVV 65


                  ..
gi 1379640789  97 IV 98
Cdd:cd01731    66 FI 67
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 17-98 2.47e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 36.52  E-value: 2.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379640789  17 PLSVLYMSVrnNTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREMwtevpKTGKGKKKaqpvnkdrfISKMFLRGDSVI 96
Cdd:PRK00737    5 PLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGEVVRK---------LGKVVIRGDNVV 68


                  ..
gi 1379640789  97 IV 98
Cdd:PRK00737   69 YV 70
LSm11_M cd01739
Like-Sm protein 11, middle domain; The eukaryotic Sm and Sm-like (LSm) proteins associate with ...
 25-67 1.53e-03

Like-Sm protein 11, middle domain; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.


Pssm-ID: 212485  Cd Length: 63  Bit Score: 34.16  E-value: 1.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1379640789  25 VRNNTQVLINCRNNKKLLGRV----MAFDRHCNMVLENVREMWTEVP 67
Cdd:cd01739     5 MRDRTRVKVYIRKAKGIRGSCegylVAFDKHWNLALVDVDETWTRRK 51
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 41-96 5.85e-03

Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212464  Cd Length: 80  Bit Score: 32.91  E-value: 5.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1379640789  41 LLGRVMAFDRHCNMVLENVREmwtEVPKTGKGKKKAQPVNKDRFISKMFLRGDSVI 96
Cdd:cd01717    23 FVGTFLAFDKHMNLVLSDCEE---FRKIKPKKKKKGEEREEKRVLGLVLLRGENVV 75
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 28-77 9.11e-03

Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.


Pssm-ID: 212479 [Multi-domain]  Cd Length: 76  Bit Score: 32.22  E-value: 9.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1379640789  28 NTQVLINCRNNKKLLGRVMAFDRHCNMVLENVREmWTEVPKTGKGKKKAQ 77
Cdd:cd01732    13 GSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTE-YEITPEGRKITKLDQ 61
 
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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