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Conserved domains on  [gi|531990788|ref|NP_001269080|]
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vacuolar protein sorting-associated protein 29 isoform 4 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MPP_superfamily super family cl13995
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
2-89 1.12e-44

metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


The actual alignment was detected with superfamily member cd07394:

Pssm-ID: 353799  Cd Length: 178  Bit Score: 141.58  E-value: 1.12e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531990788   2 LVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDEKH----YSIICVDGYP 77
Cdd:cd07394    1 LVLVIGDLHIPHRASDLPAKFKKLLVPGKIQHVLCTGNLCSKETYDYLKTIAPDVHIVRGDFDENLnypeTKVITVGQFK 80
                         90
                 ....*....|...
gi 531990788  78 -GFYSGHLCVSAN 89
Cdd:cd07394   81 iGLIHGHQVVPWG 93
 
Name Accession Description Interval E-value
MPP_Vps29 cd07394
Homo sapiens Vps29 and related proteins, metallophosphatase domain; Vps29 (vacuolar sorting ...
2-89 1.12e-44

Homo sapiens Vps29 and related proteins, metallophosphatase domain; Vps29 (vacuolar sorting protein 29), also known as vacuolar membrane protein Pep11, is a subunit of the retromer complex which is responsible for the retrieval of mannose-6-phosphate receptors (MPRs) from the endosomes for retrograde transport back to the Golgi. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer complex assembly as well as a phosphatase with specificity for the cytoplasmic tail of the MPR. The retromer includes the following 5 subunits: Vps35, Vps26, Vps29, and a dimer of the sorting nexins Vps5 (Snx1), and Vps17 (Snx2). Vps29 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 163637  Cd Length: 178  Bit Score: 141.58  E-value: 1.12e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531990788   2 LVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDEKH----YSIICVDGYP 77
Cdd:cd07394    1 LVLVIGDLHIPHRASDLPAKFKKLLVPGKIQHVLCTGNLCSKETYDYLKTIAPDVHIVRGDFDENLnypeTKVITVGQFK 80
                         90
                 ....*....|...
gi 531990788  78 -GFYSGHLCVSAN 89
Cdd:cd07394   81 iGLIHGHQVVPWG 93
Metallophos_2 pfam12850
Calcineurin-like phosphoesterase superfamily domain; Members of this family are part of the ...
1-77 6.53e-06

Calcineurin-like phosphoesterase superfamily domain; Members of this family are part of the Calcineurin-like phosphoesterase superfamily.


Pssm-ID: 338521 [Multi-domain]  Cd Length: 153  Bit Score: 41.53  E-value: 6.53e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 531990788    1 MLVLVLGDLHiphRCNSLPAKFKKLLVpGKIQHILCTGNLCTKESYDYLKTLAgDVHIVRGDFDEKHYSIICVDGYP 77
Cdd:pfam12850   1 MKIGIISDTH---DNLDALEAVLERLQ-GAVDLIIHAGDIVAPEVLEELLELA-PVLAVRGNNDLGRAAAEFGTDLP 72
yfcE TIGR00040
phosphoesterase, MJ0936 family; Members of this largely uncharacterized family share a motif ...
1-64 1.14e-05

phosphoesterase, MJ0936 family; Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown () to act on model phosphodiesterase substrates; a divalent cation was required. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 272869 [Multi-domain]  Cd Length: 158  Bit Score: 40.82  E-value: 1.14e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 531990788    1 MLVLVLGDLHIPHRCNSLPAKFKKLLVpgKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFD 64
Cdd:TIGR00040   1 MKILVISDTHGPLRATELPVELFNLES--NVDLVIHAGDLTSPFVLKEFEDLAAKVIAVRGNND 62
YfcE COG0622
Predicted phosphodiesterase [General function prediction only];
1-64 1.38e-05

Predicted phosphodiesterase [General function prediction only];


Pssm-ID: 223695 [Multi-domain]  Cd Length: 172  Bit Score: 40.80  E-value: 1.38e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 531990788   1 MLVLVLGDLHIPhrcNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYL-KTLAGDVHIVRGDFD 64
Cdd:COG0622    2 MKILVISDTHGP---LRAIEKALKIFNLEKVDAVIHAGDSTSPFTLDALeGGLAAKLIAVRGNCD 63
 
Name Accession Description Interval E-value
MPP_Vps29 cd07394
Homo sapiens Vps29 and related proteins, metallophosphatase domain; Vps29 (vacuolar sorting ...
2-89 1.12e-44

Homo sapiens Vps29 and related proteins, metallophosphatase domain; Vps29 (vacuolar sorting protein 29), also known as vacuolar membrane protein Pep11, is a subunit of the retromer complex which is responsible for the retrieval of mannose-6-phosphate receptors (MPRs) from the endosomes for retrograde transport back to the Golgi. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer complex assembly as well as a phosphatase with specificity for the cytoplasmic tail of the MPR. The retromer includes the following 5 subunits: Vps35, Vps26, Vps29, and a dimer of the sorting nexins Vps5 (Snx1), and Vps17 (Snx2). Vps29 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 163637  Cd Length: 178  Bit Score: 141.58  E-value: 1.12e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531990788   2 LVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDEKH----YSIICVDGYP 77
Cdd:cd07394    1 LVLVIGDLHIPHRASDLPAKFKKLLVPGKIQHVLCTGNLCSKETYDYLKTIAPDVHIVRGDFDENLnypeTKVITVGQFK 80
                         90
                 ....*....|...
gi 531990788  78 -GFYSGHLCVSAN 89
Cdd:cd07394   81 iGLIHGHQVVPWG 93
Metallophos_2 pfam12850
Calcineurin-like phosphoesterase superfamily domain; Members of this family are part of the ...
1-77 6.53e-06

Calcineurin-like phosphoesterase superfamily domain; Members of this family are part of the Calcineurin-like phosphoesterase superfamily.


Pssm-ID: 338521 [Multi-domain]  Cd Length: 153  Bit Score: 41.53  E-value: 6.53e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 531990788    1 MLVLVLGDLHiphRCNSLPAKFKKLLVpGKIQHILCTGNLCTKESYDYLKTLAgDVHIVRGDFDEKHYSIICVDGYP 77
Cdd:pfam12850   1 MKIGIISDTH---DNLDALEAVLERLQ-GAVDLIIHAGDIVAPEVLEELLELA-PVLAVRGNNDLGRAAAEFGTDLP 72
yfcE TIGR00040
phosphoesterase, MJ0936 family; Members of this largely uncharacterized family share a motif ...
1-64 1.14e-05

phosphoesterase, MJ0936 family; Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown () to act on model phosphodiesterase substrates; a divalent cation was required. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 272869 [Multi-domain]  Cd Length: 158  Bit Score: 40.82  E-value: 1.14e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 531990788    1 MLVLVLGDLHIPHRCNSLPAKFKKLLVpgKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFD 64
Cdd:TIGR00040   1 MKILVISDTHGPLRATELPVELFNLES--NVDLVIHAGDLTSPFVLKEFEDLAAKVIAVRGNND 62
YfcE COG0622
Predicted phosphodiesterase [General function prediction only];
1-64 1.38e-05

Predicted phosphodiesterase [General function prediction only];


Pssm-ID: 223695 [Multi-domain]  Cd Length: 172  Bit Score: 40.80  E-value: 1.38e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 531990788   1 MLVLVLGDLHIPhrcNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYL-KTLAGDVHIVRGDFD 64
Cdd:COG0622    2 MKILVISDTHGP---LRAIEKALKIFNLEKVDAVIHAGDSTSPFTLDALeGGLAAKLIAVRGNCD 63
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
1-64 3.00e-05

Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.


Pssm-ID: 333878 [Multi-domain]  Cd Length: 79  Bit Score: 38.52  E-value: 3.00e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 531990788   1 MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDY-------LKTLAGDVHIVRGDFD 64
Cdd:pfam00149  1 MRILVIGDLHGPGQLDDLLELLKKLLEEEKPDLVLHAGDLVDRGPWETevlelleRLIAYVPVYLVRGNHD 71
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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