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Conserved domains on  [gi|1958804842|ref|XP_038940460|]
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VIP36-like protein isoform X2 [Rattus norvegicus]

Protein Classification

L-type lectin family protein( domain architecture ID 46946)

L-type (leguminous) lectin family protein binds carbohydrates using a a dome-shaped beta-barrel carbohydrate recognition domain

CATH:  2.60.120.200
Gene Ontology:  GO:0030246|GO:0046872
PubMed:  14572026|14533788
SCOP:  4000327

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
lectin_L-type super family cl14058
legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate ...
 16-145 6.16e-73

legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind. This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely.


The actual alignment was detected with superfamily member cd06901:

Pssm-ID: 472686  Cd Length: 248  Bit Score: 220.34  E-value: 6.16e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  16 QRVFPYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMDIDGRHEWRDCIEMPGVRLPRG 95
Cdd:cd06901   118 EHVHPYISAMVNNGSLSYDHDRDGTHTELAGCSAPFRNKDHDTFVAIRYSKGRLTVMTDIDGKNEWKECFDVTGVRLPTG 197

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958804842  96 YYFGTSSITGDLSDNHDVISLKLFELTGVRTPEEEKLHRDVFLPSVDNLK 145
Cdd:cd06901   198 YYFGASAATGDLSDNHDIISMKLYELDVEETPEEEEIDWSKIVPSVSYLK 247
 
Name Accession Description Interval E-value
lectin_VIP36_VIPL cd06901
VIP36 and VIPL type 1 transmembrane proteins, lectin domain; The vesicular integral protein of ...
 16-145 6.16e-73

VIP36 and VIPL type 1 transmembrane proteins, lectin domain; The vesicular integral protein of 36 kDa (VIP36) is a type 1 transmembrane protein of the mammalian early secretory pathway that acts as a cargo receptor transporting high mannose type glycoproteins between the Golgi and the endoplasmic reticulum (ER). Lectins of the early secretory pathway are involved in the selective transport of newly synthesized glycoproteins from the ER to the ER-Golgi intermediate compartment (ERGIC). The most prominent cycling lectin is the mannose-binding type1 membrane protein ERGIC-53, which functions as a cargo receptor to facilitate export of glycoproteins from the ER. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely.


Pssm-ID: 173889  Cd Length: 248  Bit Score: 220.34  E-value: 6.16e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  16 QRVFPYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMDIDGRHEWRDCIEMPGVRLPRG 95
Cdd:cd06901   118 EHVHPYISAMVNNGSLSYDHDRDGTHTELAGCSAPFRNKDHDTFVAIRYSKGRLTVMTDIDGKNEWKECFDVTGVRLPTG 197

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958804842  96 YYFGTSSITGDLSDNHDVISLKLFELTGVRTPEEEKLHRDVFLPSVDNLK 145
Cdd:cd06901   198 YYFGASAATGDLSDNHDIISMKLYELDVEETPEEEEIDWSKIVPSVSYLK 247
Lectin_leg-like pfam03388
Legume-like lectin family; Lectins are structurally diverse proteins that bind to specific ...
 16-122 1.11e-40

Legume-like lectin family; Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first recognized members of a family of animal lectins similar (19-24%) to the leguminous plant lectins. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localized to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway.


Pssm-ID: 397453  Cd Length: 226  Bit Score: 137.57  E-value: 1.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  16 QRVFPYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMDI---DGRHEWRDCIEMPGVRL 92
Cdd:pfam03388 116 GPLFPYISGMLNDGSKPYDHDKDGTHQELASCTADFRNKDYPTLIRIKYDNNTLTVMIDNgllENKVDWKLCFQVNNVIL 195

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958804842  93 PRGYYFGTSSITGDLSDNHDVISLKLFELT 122
Cdd:pfam03388 196 PTGYYFGVSAQTGDLSDNHDIFSILTFQLT 225
 
Name Accession Description Interval E-value
lectin_VIP36_VIPL cd06901
VIP36 and VIPL type 1 transmembrane proteins, lectin domain; The vesicular integral protein of ...
 16-145 6.16e-73

VIP36 and VIPL type 1 transmembrane proteins, lectin domain; The vesicular integral protein of 36 kDa (VIP36) is a type 1 transmembrane protein of the mammalian early secretory pathway that acts as a cargo receptor transporting high mannose type glycoproteins between the Golgi and the endoplasmic reticulum (ER). Lectins of the early secretory pathway are involved in the selective transport of newly synthesized glycoproteins from the ER to the ER-Golgi intermediate compartment (ERGIC). The most prominent cycling lectin is the mannose-binding type1 membrane protein ERGIC-53, which functions as a cargo receptor to facilitate export of glycoproteins from the ER. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely.


Pssm-ID: 173889  Cd Length: 248  Bit Score: 220.34  E-value: 6.16e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  16 QRVFPYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMDIDGRHEWRDCIEMPGVRLPRG 95
Cdd:cd06901   118 EHVHPYISAMVNNGSLSYDHDRDGTHTELAGCSAPFRNKDHDTFVAIRYSKGRLTVMTDIDGKNEWKECFDVTGVRLPTG 197

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958804842  96 YYFGTSSITGDLSDNHDVISLKLFELTGVRTPEEEKLHRDVFLPSVDNLK 145
Cdd:cd06901   198 YYFGASAATGDLSDNHDIISMKLYELDVEETPEEEEIDWSKIVPSVSYLK 247
Lectin_leg-like pfam03388
Legume-like lectin family; Lectins are structurally diverse proteins that bind to specific ...
 16-122 1.11e-40

Legume-like lectin family; Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first recognized members of a family of animal lectins similar (19-24%) to the leguminous plant lectins. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localized to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway.


Pssm-ID: 397453  Cd Length: 226  Bit Score: 137.57  E-value: 1.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  16 QRVFPYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMDI---DGRHEWRDCIEMPGVRL 92
Cdd:pfam03388 116 GPLFPYISGMLNDGSKPYDHDKDGTHQELASCTADFRNKDYPTLIRIKYDNNTLTVMIDNgllENKVDWKLCFQVNNVIL 195

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958804842  93 PRGYYFGTSSITGDLSDNHDVISLKLFELT 122
Cdd:pfam03388 196 PTGYYFGVSAQTGDLSDNHDIFSILTFQLT 225
lectin_leg-like cd07308
legume-like lectins: ERGIC-53, ERGL, VIP36, VIPL, EMP46, and EMP47; The legume-like (leg-like) ...
 17-121 1.38e-27

legume-like lectins: ERGIC-53, ERGL, VIP36, VIPL, EMP46, and EMP47; The legume-like (leg-like) lectins are eukaryotic intracellular sugar transport proteins with a carbohydrate recognition domain similar to that of the legume lectins. This domain binds high-mannose-type oligosaccharides for transport from the endoplasmic reticulum to the Golgi complex. These leg-like lectins include ERGIC-53, ERGL, VIP36, VIPL, EMP46, EMP47, and the UIP5 (ULP1-interacting protein 5) precursor protein. Leg-like lectins have different intracellular distributions and dynamics in the endoplasmic reticulum-Golgi system of the secretory pathway and interact with N-glycans of glycoproteins in a calcium-dependent manner, suggesting a role in glycoprotein sorting and trafficking. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely.


Pssm-ID: 173892  Cd Length: 218  Bit Score: 103.59  E-value: 1.38e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  17 RVFPYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMDIDGRHEWRDCIEMPGVRLPRGY 96
Cdd:cd07308   114 KGFPSISVFLNDGTKSYDYETDGEKLELASCSLKFRNSNAPTTLRISYLNNTLKVDITYSEGNNWKECFTVEDVILPSQG 193

                          90       100
                  ....*....|....*....|....*
gi 1958804842  97 YFGTSSITGDLSDNHDVISLKLFEL 121
Cdd:cd07308   194 YFGFSAQTGDLSDNHDILSVHTYEL 218
lectin_ERGIC-53_ERGL cd06902
ERGIC-53 and ERGL type 1 transmembrane proteins, N-terminal lectin domain; ERGIC-53 and ERGL, ...
 20-122 1.31e-23

ERGIC-53 and ERGL type 1 transmembrane proteins, N-terminal lectin domain; ERGIC-53 and ERGL, N-terminal carbohydrate recognition domain. ERGIC-53 and ERGL are eukaryotic mannose-binding type 1 transmembrane proteins of the early secretory pathway that transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC). ERGIC-53 and ERGL have an N-terminal lectin-like carbohydrate recognition domain (represented by this alignment model) as well as a C-terminal transmembrane domain. ERGIC-53 functions as a 'cargo receptor' to facilitate the export of glycoproteins with different characteristics from the ER, while the ERGIC-53-like protein (ERGL) which may act as a regulator of ERGIC-53. In mammals, ERGIC-53 forms a complex with MCFD2 (multi-coagulation factor deficiency 2) which then recruits blood coagulation factors V and VIII. Mutations in either MCFD2 or ERGIC-53 cause a mild form of inherited hemophilia known as combined deficiency of factors V and VIII (F5F8D). In addition to the lectin and transmembrane domains, ERGIC-53 and ERGL have a short N-terminal cytoplasmic region of about 12 amino acids. ERGIC-53 forms disulphide-linked homodimers and homohexamers. ERGIC-53 and ERGL are sequence-similar to the lectins of leguminous plants. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely.


Pssm-ID: 173890  Cd Length: 225  Bit Score: 93.16  E-value: 1.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  20 PYISAMVNNGSLSYDHERDGRPTELGGCTAIVRNIRYDTFLVIRYVKRHLTIMMD---IDGRHEWRDCIEMPGVRLPRGY 96
Cdd:cd06902   120 PAILVVGNDGTKSYDHQNDGLTQALGSCLRDFRNKPYPVRAKITYYQNVLTVSINngfTPNKDDYELCTRVENMVLPPNG 199

                          90       100
                  ....*....|....*....|....*.
gi 1958804842  97 YFGTSSITGDLSDNHDVISLKLFELT 122
Cdd:cd06902   200 YFGVSAATGGLADDHDVLSFLTFSLT 225
lectin_L-type cd01951
legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate ...
 19-120 1.57e-04

legume lectins; The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind. This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely.


Pssm-ID: 173886 [Multi-domain]  Cd Length: 223  Bit Score: 40.88  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804842  19 FPYISAMVNNGSLSYDHerdgrPTELGGCTA-IVRNIRYDTFLVIRYVK--RHLTIMMDiDGRHEWRDCIEMP---GVRL 92
Cdd:cd01951   122 GNHISIDVNGNGNNTAL-----ATSLGSASLpNGTGLGNEHTVRITYDPttNTLTVYLD-NGSTLTSLDITIPvdlIQLG 195

                          90       100
                  ....*....|....*....|....*...
gi 1958804842  93 PRGYYFGTSSITGDLSDNHDVISLKLFE 120
Cdd:cd01951   196 PTKAYFGFTASTGGLTNLHDILNWSFTS 223
 
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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