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Conserved domains on  [gi|15237740|ref|NP_200680|]
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smr (Small MutS Related) domain-containing protein [Arabidopsis thaliana]

Protein Classification

NEDD4-binding protein 2; putative nuclear RNA export factor SDE5( domain architecture ID 10406529)

NEDD4-binding protein 2 (N4BP2) has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination| protein SILENCING DEFECTIVE 5 (SDE5) is a DUF1771 domain-containing protein that acts as a putative nuclear RNA export factor involved in sense transgene post-transcriptional gene silencing (S-PTGS)

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DUF1771 pfam08590
Domain of unknown function (DUF1771); This domain is highly charged and may represent a small ...
358-419 7.80e-16

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.


:

Pssm-ID: 462528  Cd Length: 62  Bit Score: 71.78  E-value: 7.80e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237740   358 ELRKGANDQWNVTKSYYQKAAEAYSKGGRAHAAYLSDKGRVASKQAQRADERASQDIFVARN 419
Cdd:pfam08590   1 RLRAEARKHARKRNELFQKAAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62
SMR smart00463
Small MutS-related domain;
427-501 1.30e-15

Small MutS-related domain;


:

Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 71.56  E-value: 1.30e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237740    427 TIDLHGQHVKPAMKLLKLHLLFGSYVPSIQTLRVITGCGASGF-GKSKVKQSVVKLLEREGVRYCEE-NRGTLLIKL 501
Cdd:smart00463   3 SLDLHGLTVEEALTALDKFLNNARLKGLEQKLVIITGKGKHSLgGKSGVKPALKEHLRVESFRFAEEgNSGVLVVKL 79
UBA_like_SF super family cl21463
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ...
187-227 3.72e-06

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.


The actual alignment was detected with superfamily member cd14365:

Pssm-ID: 473871  Cd Length: 42  Bit Score: 43.81  E-value: 3.72e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 15237740 187 REKAEQFLSSMLGDDceLSMAVVRDVLCQCGYDVDMALNVL 227
Cdd:cd14365   1 QEELFQQLQEMFSGK--LDPSVVYMVLSECDFKVDNAMDTL 39
 
Name Accession Description Interval E-value
DUF1771 pfam08590
Domain of unknown function (DUF1771); This domain is highly charged and may represent a small ...
358-419 7.80e-16

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.


Pssm-ID: 462528  Cd Length: 62  Bit Score: 71.78  E-value: 7.80e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237740   358 ELRKGANDQWNVTKSYYQKAAEAYSKGGRAHAAYLSDKGRVASKQAQRADERASQDIFVARN 419
Cdd:pfam08590   1 RLRAEARKHARKRNELFQKAAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62
SMR smart00463
Small MutS-related domain;
427-501 1.30e-15

Small MutS-related domain;


Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 71.56  E-value: 1.30e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237740    427 TIDLHGQHVKPAMKLLKLHLLFGSYVPSIQTLRVITGCGASGF-GKSKVKQSVVKLLEREGVRYCEE-NRGTLLIKL 501
Cdd:smart00463   3 SLDLHGLTVEEALTALDKFLNNARLKGLEQKLVIITGKGKHSLgGKSGVKPALKEHLRVESFRFAEEgNSGVLVVKL 79
CUE_N4BP2 cd14365
CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins; N4BP2 has been ...
187-227 3.72e-06

CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins; N4BP2 has been identified as an oncogene bcl-3 coding protein BCL-3-binding protein (B3BP) that participates in connecting transcriptional activation and genetic recombination of the Ig gene. In addition to BCL-3, it also interacts with p300/CBP histone acetyltransferases. N4BP2 shows intrinsic ATP binding and hydrolyzing activity. It contains an N-terminal ATP-binding region that is responsible for the interaction with BCL-3 and p300/CBP. N4BP2 also functions as a 5'-polynucleotide kinase that can transfer a phosphate group to the 5' end of DNA and RNA substrates. Moreover, N4BP2 contains a C-terminal MutS-related domain that possesses nicking endonuclease activity and may play a role in DNA mismatch repair (MMR). This model corresponds to CUE domain in the N-terminus of N4BP2.


Pssm-ID: 270548  Cd Length: 42  Bit Score: 43.81  E-value: 3.72e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 15237740 187 REKAEQFLSSMLGDDceLSMAVVRDVLCQCGYDVDMALNVL 227
Cdd:cd14365   1 QEELFQQLQEMFSGK--LDPSVVYMVLSECDFKVDNAMDTL 39
 
Name Accession Description Interval E-value
DUF1771 pfam08590
Domain of unknown function (DUF1771); This domain is highly charged and may represent a small ...
358-419 7.80e-16

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.


Pssm-ID: 462528  Cd Length: 62  Bit Score: 71.78  E-value: 7.80e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237740   358 ELRKGANDQWNVTKSYYQKAAEAYSKGGRAHAAYLSDKGRVASKQAQRADERASQDIFVARN 419
Cdd:pfam08590   1 RLRAEARKHARKRNELFQKAAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62
SMR smart00463
Small MutS-related domain;
427-501 1.30e-15

Small MutS-related domain;


Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 71.56  E-value: 1.30e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237740    427 TIDLHGQHVKPAMKLLKLHLLFGSYVPSIQTLRVITGCGASGF-GKSKVKQSVVKLLEREGVRYCEE-NRGTLLIKL 501
Cdd:smart00463   3 SLDLHGLTVEEALTALDKFLNNARLKGLEQKLVIITGKGKHSLgGKSGVKPALKEHLRVESFRFAEEgNSGVLVVKL 79
CUE_N4BP2 cd14365
CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins; N4BP2 has been ...
187-227 3.72e-06

CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins; N4BP2 has been identified as an oncogene bcl-3 coding protein BCL-3-binding protein (B3BP) that participates in connecting transcriptional activation and genetic recombination of the Ig gene. In addition to BCL-3, it also interacts with p300/CBP histone acetyltransferases. N4BP2 shows intrinsic ATP binding and hydrolyzing activity. It contains an N-terminal ATP-binding region that is responsible for the interaction with BCL-3 and p300/CBP. N4BP2 also functions as a 5'-polynucleotide kinase that can transfer a phosphate group to the 5' end of DNA and RNA substrates. Moreover, N4BP2 contains a C-terminal MutS-related domain that possesses nicking endonuclease activity and may play a role in DNA mismatch repair (MMR). This model corresponds to CUE domain in the N-terminus of N4BP2.


Pssm-ID: 270548  Cd Length: 42  Bit Score: 43.81  E-value: 3.72e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 15237740 187 REKAEQFLSSMLGDDceLSMAVVRDVLCQCGYDVDMALNVL 227
Cdd:cd14365   1 QEELFQQLQEMFSGK--LDPSVVYMVLSECDFKVDNAMDTL 39
 
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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