Summary: Sugar-binding N-terminal domain
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Sugar-binding N-terminal domain Provide feedback
This is the N-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain [1]. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity [2]. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK) [1].
Literature references
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Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V, Jacobson MP, Almo SC, Gerlt JA;, Proc Natl Acad Sci U S A. 2016;113:E4161-E4169.: Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. PUBMED:27402745 EPMC:27402745
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Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Crecy-Lagard V;, ACS Chem Biol. 2016;11:2304-2311.: Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. PUBMED:27294475 EPMC:27294475
This tab holds annotation information from the InterPro database.
InterPro entry IPR010737
This conserved region is found in four-carbon acid sugar kinases from a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. These four-carbon acid sugar kinases are composed of two domains: an N-terminal domain and a C-terminal domain connected by a variable linker sequence. The N-terminal domain exhibits an alpha/beta-fold composed of an eight-stranded parallel beta-sheet. The C-terminal domain also exhibits an alpha/beta-fold composed of a seven-stranded mixed beta-sheet. The acid sugar is bound by the N-terminal domain, while nucleotide by the C-terminal domain [PUBMED:27402745].
Proteins containing this domain include 3-oxo-tetronate kinase from Methylobacterium radiotolerans, D-threonate kinase from Bordetella bronchiseptica and D-erythronate kinase from Heliobacterium modesticaldum [PUBMED:27402745].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Alignments
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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 (229) |
Full (3151) |
Representative proteomes | UniProt (14088) |
NCBI (24118) |
Meta (273) |
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RP15 (213) |
RP35 (1335) |
RP55 (3053) |
RP75 (5674) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (229) |
Full (3151) |
Representative proteomes | UniProt (14088) |
NCBI (24118) |
Meta (273) |
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RP15 (213) |
RP35 (1335) |
RP55 (3053) |
RP75 (5674) |
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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: | Pfam-B_8609 (release 10.0) |
Previous IDs: | Hop; PF07005; DUF1537; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Vella Briffa B |
Number in seed: | 229 |
Number in full: | 3151 |
Average length of the domain: | 222.20 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 45.09 % |
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: | 228 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
SBD_NStructures
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 SBD_N domain has been found. There are 11 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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