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Conserved domains on  [gi|1877256356|dbj|BBQ19106|]
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hypothetical protein WP2S17E02_P30010 (plasmid) [Klebsiella pneumoniae]

Protein Classification

NYN domain-containing protein( domain architecture ID 13036802)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_NicB-like cd18722
LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from ...
 2-174 4.71e-35

LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from Pseudomonas putida S16 is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine. This subfamily also includes the uncharacterized CPP15 (plasmid) protein from Campylobacter jejuni. 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: 350289  Cd Length: 117  Bit Score: 120.74  E-value: 4.71e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356   2 RTIVYVDGFNFYHGLVKRSG-----YKWLDLYKLFEEQLLPIRAREsQLIQVKFFTAEIKAKFAsqgelahqaqqayhra 76
Cdd:cd18722     1 RTAVYVDGFNLYYGLKAREElklyrYYWLDLPPLAKNLLLPDPSQE-LLERVKYFTARVNSSPK---------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356  77 lvqiygdklqiikgyyserqecamtfnegqppsktdrttvwklEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPP 156
Cdd:cd18722    64 -------------------------------------------EEKGVDVNIALDILSDAYKKQVDQAVLVSGDSDFVPA 100

                         170
                  ....*....|....*...
gi 1877256356 157 IEMIKAdRPELKIGIVVP 174
Cdd:cd18722   101 VKLARR-EPGIRVGLAFP 117
 
Name Accession Description Interval E-value
PIN_NicB-like cd18722
LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from ...
 2-174 4.71e-35

LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from Pseudomonas putida S16 is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine. This subfamily also includes the uncharacterized CPP15 (plasmid) protein from Campylobacter jejuni. 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: 350289  Cd Length: 117  Bit Score: 120.74  E-value: 4.71e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356   2 RTIVYVDGFNFYHGLVKRSG-----YKWLDLYKLFEEQLLPIRAREsQLIQVKFFTAEIKAKFAsqgelahqaqqayhra 76
Cdd:cd18722     1 RTAVYVDGFNLYYGLKAREElklyrYYWLDLPPLAKNLLLPDPSQE-LLERVKYFTARVNSSPK---------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356  77 lvqiygdklqiikgyyserqecamtfnegqppsktdrttvwklEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPP 156
Cdd:cd18722    64 -------------------------------------------EEKGVDVNIALDILSDAYKKQVDQAVLVSGDSDFVPA 100

                         170
                  ....*....|....*...
gi 1877256356 157 IEMIKAdRPELKIGIVVP 174
Cdd:cd18722   101 VKLARR-EPGIRVGLAFP 117
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 1-162 9.52e-10

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


Pssm-ID: 441041  Cd Length: 164  Bit Score: 55.67  E-value: 9.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356   1 MRTIVYVDGFNFYHGLvkRSGYKWLDLYKLFEEqlLpirARESQLIQVKFFTAEikakfasqgelAHQAQQAYHRALVQI 80
Cdd:COG1432     1 KRVAVFIDGDNLYAAA--RDLGFDIDYEKLLEE--L---AEYGRLVRARAYGDD-----------TDERQQGFIDALREN 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356  81 YgdkLQIIKGYYSERqecamtfnegqppsktdRTTvwklEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMI 160
Cdd:COG1432    63 G---FEVILKPLQQF-----------------RTS----GKNAVDVELAVDAMELAYTPNIDTFVLVSGDSDFTPLVERL 118


                  ..
gi 1877256356 161 KA 162
Cdd:COG1432   119 RE 120
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 121-162 2.26e-03

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: 36.88  E-value: 2.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1877256356 121 EKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKA 162
Cdd:pfam01936  69 KNAVDVGLAVDALELAYDNNPDTFVLVSGDGDFAPLLERLRE 110
 
Name Accession Description Interval E-value
PIN_NicB-like cd18722
LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from ...
 2-174 4.71e-35

LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from Pseudomonas putida S16 is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine. This subfamily also includes the uncharacterized CPP15 (plasmid) protein from Campylobacter jejuni. 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: 350289  Cd Length: 117  Bit Score: 120.74  E-value: 4.71e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356   2 RTIVYVDGFNFYHGLVKRSG-----YKWLDLYKLFEEQLLPIRAREsQLIQVKFFTAEIKAKFAsqgelahqaqqayhra 76
Cdd:cd18722     1 RTAVYVDGFNLYYGLKAREElklyrYYWLDLPPLAKNLLLPDPSQE-LLERVKYFTARVNSSPK---------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356  77 lvqiygdklqiikgyyserqecamtfnegqppsktdrttvwklEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPP 156
Cdd:cd18722    64 -------------------------------------------EEKGVDVNIALDILSDAYKKQVDQAVLVSGDSDFVPA 100

                         170
                  ....*....|....*...
gi 1877256356 157 IEMIKAdRPELKIGIVVP 174
Cdd:cd18722   101 VKLARR-EPGIRVGLAFP 117
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 1-162 5.39e-10

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; This subfamily contains 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. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are 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 the LabA-like 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: 350235  Cd Length: 154  Bit Score: 55.96  E-value: 5.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356   1 MRTIVYVDGFNFYHGLvKRSGYKwLDLYKLFEEqLlpirARESQLIQVKFFTAEIKAKfasqgelaHQAQQAYHRALVQI 80
Cdd:cd10911     1 ERVAVFIDGANLYYAA-KKLGWK-IDYEKLLKY-L----VGGRELVRAYYYTAVDDEE--------DEKQQKFLDALRKI 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356  81 ygdklqiikgYYSERQECAMTFNEGQPPSKtdrttvwkleEKQTDVRMALEMYRDAIRgeAEQLVLCTNDSDMIPPIEMI 160
Cdd:cd10911    66 ----------GYEVVTKPLKEFRDEGGGSV----------KGNVDVEIAVDMLRLADK--YDTAILVSGDGDFAPLVEYL 123


                  ..
gi 1877256356 161 KA 162
Cdd:cd10911   124 QR 125
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 1-162 9.52e-10

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


Pssm-ID: 441041  Cd Length: 164  Bit Score: 55.67  E-value: 9.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356   1 MRTIVYVDGFNFYHGLvkRSGYKWLDLYKLFEEqlLpirARESQLIQVKFFTAEikakfasqgelAHQAQQAYHRALVQI 80
Cdd:COG1432     1 KRVAVFIDGDNLYAAA--RDLGFDIDYEKLLEE--L---AEYGRLVRARAYGDD-----------TDERQQGFIDALREN 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877256356  81 YgdkLQIIKGYYSERqecamtfnegqppsktdRTTvwklEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMI 160
Cdd:COG1432    63 G---FEVILKPLQQF-----------------RTS----GKNAVDVELAVDAMELAYTPNIDTFVLVSGDSDFTPLVERL 118


                  ..
gi 1877256356 161 KA 162
Cdd:COG1432   119 RE 120
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 121-162 2.26e-03

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: 36.88  E-value: 2.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1877256356 121 EKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKA 162
Cdd:pfam01936  69 KNAVDVGLAVDALELAYDNNPDTFVLVSGDGDFAPLLERLRE 110
 
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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