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Conserved domains on  [gi|568963070|ref|XP_006511847|]
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protein asteroid homolog 1 isoform X1 [Mus musculus]

Protein Classification

PIN domain-containing protein( domain architecture ID 1000090)

PIN (PilT N terminus) domain-containing protein may function as a nuclease

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_SF super family cl28905
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 28-181 2.24e-52

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. 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. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


The actual alignment was detected with superfamily member cd18676:

Pssm-ID: 475124 [Multi-domain]  Cd Length: 164  Bit Score: 177.84  E-value: 2.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568963070  28 LIIDGYSLFHRLCFNSDLELR-YGGDYDLFADVVQKFFESLFVCHICPYVVLDGGCDISDKKLTTLKDRAKEKIQAARSL 106
Cdd:cd18676    1 LVIDGNNLCYQLYFDSNLDNSaFGGDYDKYARVVREFFELLSKCNVTPYVILDGGYEDRKLKTVTSRLRAKIKIAKAKTP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568963070 107 SLGGGGNVCPLLIREVFIQVLIRLEVCFVQSFSEADRDIMTLANHWNCPVLSSDSDFCIFDlrSGFCSLNSFQWR 181
Cdd:cd18676   81 STGGSGSILPLLLKEVFVDVLKELNVKVVQCDFEADDEIAALARKLNCPVLSYDSDFYIFD--VLYIPFSTVQWN 153
 
Name Accession Description Interval E-value
PIN_asteroid-like cd18676
FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily ...
 28-181 2.24e-52

FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily includes Drosophila melanogaster asteroid protein which may function in EGF receptor signaling, and may play a role in compound eye morphogenesis. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), 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: 350243 [Multi-domain]  Cd Length: 164  Bit Score: 177.84  E-value: 2.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568963070  28 LIIDGYSLFHRLCFNSDLELR-YGGDYDLFADVVQKFFESLFVCHICPYVVLDGGCDISDKKLTTLKDRAKEKIQAARSL 106
Cdd:cd18676    1 LVIDGNNLCYQLYFDSNLDNSaFGGDYDKYARVVREFFELLSKCNVTPYVILDGGYEDRKLKTVTSRLRAKIKIAKAKTP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568963070 107 SLGGGGNVCPLLIREVFIQVLIRLEVCFVQSFSEADRDIMTLANHWNCPVLSSDSDFCIFDlrSGFCSLNSFQWR 181
Cdd:cd18676   81 STGGSGSILPLLLKEVFVDVLKELNVKVVQCDFEADDEIAALARKLNCPVLSYDSDFYIFD--VLYIPFSTVQWN 153
 
Name Accession Description Interval E-value
PIN_asteroid-like cd18676
FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily ...
 28-181 2.24e-52

FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily includes Drosophila melanogaster asteroid protein which may function in EGF receptor signaling, and may play a role in compound eye morphogenesis. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), 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: 350243 [Multi-domain]  Cd Length: 164  Bit Score: 177.84  E-value: 2.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568963070  28 LIIDGYSLFHRLCFNSDLELR-YGGDYDLFADVVQKFFESLFVCHICPYVVLDGGCDISDKKLTTLKDRAKEKIQAARSL 106
Cdd:cd18676    1 LVIDGNNLCYQLYFDSNLDNSaFGGDYDKYARVVREFFELLSKCNVTPYVILDGGYEDRKLKTVTSRLRAKIKIAKAKTP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568963070 107 SLGGGGNVCPLLIREVFIQVLIRLEVCFVQSFSEADRDIMTLANHWNCPVLSSDSDFCIFDlrSGFCSLNSFQWR 181
Cdd:cd18676   81 STGGSGSILPLLLKEVFVDVLKELNVKVVQCDFEADDEIAALARKLNCPVLSYDSDFYIFD--VLYIPFSTVQWN 153
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-142 3.32e-08

FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), 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. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 54.33  E-value: 3.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568963070   1 MGIRGLMSFVEDYSNEFFVDlKLRNTKLIIDGYSLFHRLCFNSDLELRYGGDYDLFADVVQKFFESLFVCHICPYVVLDg 80
Cdd:cd09857    1 MGIQGLLPFLKPIQRPVHIS-EYAGKTVAVDAYCWLHRGAYSCAEELALGKPTDKYIDYCMKRVNMLLHHGITPILVFD- 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568963070  81 GCDISDKKLTTLK---DRAKEKIQAARSLSLG----------GGGNVCPLLIREVfIQVLIRLEVCFVQSFSEAD 142
Cdd:cd09857   79 GAPLPSKAGTEEErreRREEALEKALELLREGkksearecfqRAVDITPEMAHEL-IKALRKENVEYIVAPYEAD 152
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 29-188 1.39e-05

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), 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: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 45.94  E-value: 1.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568963070  29 IIDGYSLFHRLCF-NSDLELRYGGDYDLFADVVQKFFEsLFVCHICPYVVLDGGcdisdkklttlKDRAKEKIQAARSLS 107
Cdd:cd09853    1 VIDGMNIAFNFAHpVRNLKEEEGSDFQGYFSAVDDLVK-KLKPGIKPILLFDGG-----------KPKAKKGNRDKRRER 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568963070 108 LGGGGNVCPLLIREV--FIQVLIR-----LEVCF-----------VQSFSEADRDIMTLA-----NHWNCPVLSSDSDFC 164
Cdd:cd09853   69 RAREEDRKKGQLKEHkeFDKRLIElgpeyLIRLFellkhfmgipvMDAPGEAEDEIAYLVkkhkhLGTVHLIISTDGDFL 148

                        170       180
                 ....*....|....*....|....
gi 568963070 165 IFDLRSGFCSLNSFQWRNLNTIKD 188
Cdd:cd09853  149 LLGTDHPYIPRNLLTVKEETFQEF 172
 
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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