Summary: Galactose-binding domain-like
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Galactose-binding domain-like Provide feedback
Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase [1] phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va [2] membrane-anchored ephrin for the Eph family of receptor tyrosine kinases [3] and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1 [4]. The structure of the galactose-binding domain-like members consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold [5].
Literature references
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Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF; , Nature 1991;350:87-90.: Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. PUBMED:2002850 EPMC:2002850
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Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, Fuentes-Prior P;, Nature. 1999;402:434-439.: Crystal structures of the membrane-binding C2 domain of human coagulation factor V. PUBMED:10586886 EPMC:10586886
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Himanen JP, Rajashankar KR, Lackmann M, Cowan CA, Henkemeyer M, Nikolov DB;, Nature. 2001;414:933-938.: Crystal structure of an Eph receptor-ephrin complex. PUBMED:11780069 EPMC:11780069
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Marintchev A, Mullen MA, Maciejewski MW, Pan B, Gryk MR, Mullen GP; , Nat Struct Biol 1999;6:884-893.: Solution structure of the single-strand break repair protein XRCC1 N- terminal domain. PUBMED:10467102 EPMC:10467102
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Caines ME, Zhu H, Vuckovic M, Willis LM, Withers SG, Wakarchuk WW, Strynadka NC;, J Biol Chem. 2008;283:31279-31283.: The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design. PUBMED:18784084 EPMC:18784084
This tab holds annotation information from the InterPro database.
InterPro entry IPR040502
Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase [PUBMED:2002850], phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va [PUBMED:10586886], membrane-anchored ephrin for the Eph family of receptor tyrosine kinases [PUBMED:11780069], and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1 [PUBMED:10467102]. The structure of the galactose-binding domain-like members consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold [PUBMED:18784084].
This entry represents a galactose-binding domain-like fold domain found in endo-alpha-N-acetylgalactosaminidases from bacteria.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Concanavalin (CL0004), which has the following description:
This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.
The clan contains the following 49 members:
Alginate_lyase2 ArabFuran-catal Arabino_trans_N Bac_rhamnosid Bact_lectin bCoV_S1_N Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 Exotox-A_bind Gal-bind_lectin GalBD_like GH131_N GH43_C2 Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 HA1 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB MAM Methyltransf_FA Neuralized Pentaxin Peptidase_A4 Polysacc_lyase PRY Reoviridae_Vp9 Sial-lect-inser Sialidase SKN1 SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpDAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (16) |
Full (245) |
Representative proteomes | UniProt (1380) |
NCBI (4767) |
Meta (1) |
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RP15 (28) |
RP35 (119) |
RP55 (258) |
RP75 (457) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (16) |
Full (245) |
Representative proteomes | UniProt (1380) |
NCBI (4767) |
Meta (1) |
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RP15 (28) |
RP35 (119) |
RP55 (258) |
RP75 (457) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | ECOD:EUF00543 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
El-Gebali S |
Number in seed: | 16 |
Number in full: | 245 |
Average length of the domain: | 177.60 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 11.89 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 190 | ||||||||||||
Family (HMM) version: | 2 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GalBD_like domain has been found. There are 13 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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