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Conserved domains on  [gi|253314447|ref|NP_001156594|]
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RAD52 motif-containing protein 1 isoform 5 [Homo sapiens]

Protein Classification

RRM_RDM1 domain-containing protein( domain architecture ID 10188893)

RRM_RDM1 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
 10-72 4.62e-36

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


:

Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 122.09  E-value: 4.62e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 253314447  10 HSLFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKSPVKVRL 72
Cdd:cd12364   19 ESLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNGKWLFQGSPLKVRF 81
 
Name Accession Description Interval E-value
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
 10-72 4.62e-36

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 122.09  E-value: 4.62e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 253314447  10 HSLFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKSPVKVRL 72
Cdd:cd12364   19 ESLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNGKWLFQGSPLKVRF 81
RRM smart00360
RNA recognition motif;
12-70 4.57e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 4.57e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 253314447    12 LFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKsPVKV 70
Cdd:smart00360  16 LRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR-PLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 9-65 1.06e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 39.52  E-value: 1.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 253314447    9 QHSLFTAFSQFGLLYSVRVFPNAAVAHPGFyAVIKFYSARAAHRAQKACDRKQLFQK 65
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVRDETGRSKGF-AFVEFEDEEDAEKAIEALNGKELGGR 67
 
Name Accession Description Interval E-value
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
 10-72 4.62e-36

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 122.09  E-value: 4.62e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 253314447  10 HSLFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKSPVKVRL 72
Cdd:cd12364   19 ESLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNGKWLFQGSPLKVRF 81
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 12-71 3.33e-07

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.51  E-value: 3.33e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 253314447  12 LFTAFSQFGLLYSVRVFPNAAVAHPGfYAVIKFYSARAAHRAQKACDRKQlFQKSPVKVR 71
Cdd:cd00590   15 LRELFSKFGEVVSVRIVRDRDGKSKG-FAFVEFESPEDAEKALEALNGTE-LGGRPLKVS 72
RRM smart00360
RNA recognition motif;
12-70 4.57e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 4.57e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 253314447    12 LFTAFSQFGLLYSVRVFPNAAVAHPGFYAVIKFYSARAAHRAQKACDRKQLFQKsPVKV 70
Cdd:smart00360  16 LRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR-PLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 9-65 1.06e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 39.52  E-value: 1.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 253314447    9 QHSLFTAFSQFGLLYSVRVFPNAAVAHPGFyAVIKFYSARAAHRAQKACDRKQLFQK 65
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVRDETGRSKGF-AFVEFEDEEDAEKAIEALNGKELGGR 67
 
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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