NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|490286027|ref|WP_004181819|]
View 

MULTISPECIES: NYN domain-containing protein [Enterobacteriaceae]

Protein Classification

NYN domain-containing protein( domain architecture ID 13036840)

NYN domain-containing protein; the NYN domain shares a common protein fold with PIN (PilT N-terminal)-domain nucleases

Gene Ontology:  GO:0004540
PubMed:  17114934

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PIN_LabA-like cd18723
uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA ...
 7-116 5.92e-70

uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized 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 Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this 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. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_7.


:

Pssm-ID: 350290  Cd Length: 110  Bit Score: 209.38  E-value: 5.92e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027   7 RIALIDYENIGSLEGVSLHDFDKVLFFTGAKQENIKIPVTSLSSAISVCIIPATEVSKNNVDFHLVLELGQLTALSGDTS 86
Cdd:cd18723    1 RIALIDYENCCNLRNISLADYTDLILFAGPLQQTVVLPADTWPDNIRVSIRQIDNISKNNVDFHLVMELGRMTCCSAGNN 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 490286027  87 HFSVISRDKGYDGIIARLKAAGISCTRFSP 116
Cdd:cd18723   81 TWHIISNDKGYDGIIHTLQKRGFRCERIAP 110
 
Name Accession Description Interval E-value
PIN_LabA-like cd18723
uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA ...
 7-116 5.92e-70

uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized 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 Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this 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. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_7.


Pssm-ID: 350290  Cd Length: 110  Bit Score: 209.38  E-value: 5.92e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027   7 RIALIDYENIGSLEGVSLHDFDKVLFFTGAKQENIKIPVTSLSSAISVCIIPATEVSKNNVDFHLVLELGQLTALSGDTS 86
Cdd:cd18723    1 RIALIDYENCCNLRNISLADYTDLILFAGPLQQTVVLPADTWPDNIRVSIRQIDNISKNNVDFHLVMELGRMTCCSAGNN 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 490286027  87 HFSVISRDKGYDGIIARLKAAGISCTRFSP 116
Cdd:cd18723   81 TWHIISNDKGYDGIIHTLQKRGFRCERIAP 110
PIN7 pfam18475
PIN domain; This is a bacterial PIN-like domain of unknown function.
 10-108 2.18e-21

PIN domain; This is a bacterial PIN-like domain of unknown function.


Pssm-ID: 436528 [Multi-domain]  Cd Length: 103  Bit Score: 84.95  E-value: 2.18e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027   10 LIDYENIGSLEGVS---LHDFDKVLFFTGAKQENIKIPVTSLSSAISVCI--IPATEVSKNNVDFHLVLELGQLTALSGD 84
Cdd:pfam18475   1 LIDYENVQPKGIELielLPGYDRVIVFYGANQPKLPFELVKKLQPLGGKAeyIKIKGGGKNALDFHLAFYLGYLIAEDPE 80

                          90       100
                  ....*....|....*....|....
gi 490286027   85 tSHFSVISRDKGYDGIIARLKAAG 108
Cdd:pfam18475  81 -AEFVIISNDKGFDPLVDHWKKRG 103
 
Name Accession Description Interval E-value
PIN_LabA-like cd18723
uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA ...
 7-116 5.92e-70

uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized 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 Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this 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. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_7.


Pssm-ID: 350290  Cd Length: 110  Bit Score: 209.38  E-value: 5.92e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027   7 RIALIDYENIGSLEGVSLHDFDKVLFFTGAKQENIKIPVTSLSSAISVCIIPATEVSKNNVDFHLVLELGQLTALSGDTS 86
Cdd:cd18723    1 RIALIDYENCCNLRNISLADYTDLILFAGPLQQTVVLPADTWPDNIRVSIRQIDNISKNNVDFHLVMELGRMTCCSAGNN 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 490286027  87 HFSVISRDKGYDGIIARLKAAGISCTRFSP 116
Cdd:cd18723   81 TWHIISNDKGYDGIIHTLQKRGFRCERIAP 110
PIN7 pfam18475
PIN domain; This is a bacterial PIN-like domain of unknown function.
 10-108 2.18e-21

PIN domain; This is a bacterial PIN-like domain of unknown function.


Pssm-ID: 436528 [Multi-domain]  Cd Length: 103  Bit Score: 84.95  E-value: 2.18e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027   10 LIDYENIGSLEGVS---LHDFDKVLFFTGAKQENIKIPVTSLSSAISVCI--IPATEVSKNNVDFHLVLELGQLTALSGD 84
Cdd:pfam18475   1 LIDYENVQPKGIELielLPGYDRVIVFYGANQPKLPFELVKKLQPLGGKAeyIKIKGGGKNALDFHLAFYLGYLIAEDPE 80

                          90       100
                  ....*....|....*....|....
gi 490286027   85 tSHFSVISRDKGYDGIIARLKAAG 108
Cdd:pfam18475  81 -AEFVIISNDKGFDPLVDHWKKRG 103
PIN_LabA-like cd06167
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 8-116 3.76e-05

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. This family also includes the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Other members are the LabA-like PIN domains of 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 this family.


Pssm-ID: 350201  Cd Length: 113  Bit Score: 41.63  E-value: 3.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027   8 IALIDYEN----IGSLEGVSLHDFDKVLFFTGAKQENIKIPVTSLSsaISVCIIPATEVSK--NNVDFHLVLELGQLtAL 81
Cdd:cd06167    1 GVLVDADNcsngFGALILRRYAGLFLQMGFEKYANINAQPLLVPPS--NNRGFTVIRVAAKrkDAADVALVRQAGRL-AY 77

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 490286027  82 SGDTSHFSVISRDKgYDGIIA--RLKAAGISCTRFSP 116
Cdd:cd06167   78 TGAPDTVVLVSGDK-LDFSDLieKAKEAGLNVIVVGP 113
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 7-109 8.76e-04

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 38.42  E-value: 8.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490286027    7 RIA-LIDYENIGSLEGVslhDFDKVL-------------FFTGAKQENIKIPVTSLSS-AISVCIIPATEvSKNNVDFHL 71
Cdd:pfam01936   1 RVAvFIDGENCPLPDGV---DYRKVLeeirsggevvrarAYGNWGDPDLRKFPDALSStGIPVQHKPLTK-GKNAVDVGL 76

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 490286027   72 VLELGQLtALSGDTSHFSVISRDKGYDGIIARLKAAGI 109
Cdd:pfam01936  77 AVDALEL-AYDNNPDTFVLVSGDGDFAPLLERLRERGK 113
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH