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Conserved domains on  [gi|1063717208|ref|NP_001325516|]
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Putative endonuclease or glycosyl hydrolase [Arabidopsis thaliana]

Protein Classification

NYN domain-containing protein( domain architecture ID 10180750)

NYN domain-containing protein; the NYN domain shares a common protein fold with PIN (PilT N-terminal)-domain nucleases; similar to Human MARF1 (meiosis regulator and mRNA stability factor 1), an essential regulator of oogenesis required for female meiotic progression to repress transposable elements and preventing their mobilization, which is essential for the germline integrity

Gene Ontology:  GO:0004540
PubMed:  17114934

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_limkain_b1_N_like cd10910
N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ...
 18-114 4.86e-21

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. 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 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: 350234  Cd Length: 126  Bit Score: 82.67  E-value: 4.86e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717208  18 KTFVLWDVEVCPIPDGLGPHDVFSNIKRVLMDNGYRGDVSTTPYTDLTKSN-------------------GDRDARLEVY 78
Cdd:cd10910     1 KTGVFWDIENCPVPDGYDARRVGPNIRRALRKLGYSGPVSITAYGDLSKVPkdvlselsssgvslvhvphGGKKAADKKI 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1063717208  79 MIDLYSCVVKEDGPLNLMLFVGDIssrsKDFFRVFR 114
Cdd:cd10910    81 LVDMLLWALDNPPPANIMLISGDV----RDFAYALS 112
 
Name Accession Description Interval E-value
PIN_limkain_b1_N_like cd10910
N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ...
 18-114 4.86e-21

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. 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 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: 350234  Cd Length: 126  Bit Score: 82.67  E-value: 4.86e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717208  18 KTFVLWDVEVCPIPDGLGPHDVFSNIKRVLMDNGYRGDVSTTPYTDLTKSN-------------------GDRDARLEVY 78
Cdd:cd10910     1 KTGVFWDIENCPVPDGYDARRVGPNIRRALRKLGYSGPVSITAYGDLSKVPkdvlselsssgvslvhvphGGKKAADKKI 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1063717208  79 MIDLYSCVVKEDGPLNLMLFVGDIssrsKDFFRVFR 114
Cdd:cd10910    81 LVDMLLWALDNPPPANIMLISGDV----RDFAYALS 112
 
Name Accession Description Interval E-value
PIN_limkain_b1_N_like cd10910
N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ...
 18-114 4.86e-21

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. 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 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: 350234  Cd Length: 126  Bit Score: 82.67  E-value: 4.86e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717208  18 KTFVLWDVEVCPIPDGLGPHDVFSNIKRVLMDNGYRGDVSTTPYTDLTKSN-------------------GDRDARLEVY 78
Cdd:cd10910     1 KTGVFWDIENCPVPDGYDARRVGPNIRRALRKLGYSGPVSITAYGDLSKVPkdvlselsssgvslvhvphGGKKAADKKI 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1063717208  79 MIDLYSCVVKEDGPLNLMLFVGDIssrsKDFFRVFR 114
Cdd:cd10910    81 LVDMLLWALDNPPPANIMLISGDV----RDFAYALS 112
 
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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