Summary: Shikimate dehydrogenase substrate binding domain
Shikimate dehydrogenase substrate binding domain Provide feedback
This domain is the substrate binding domain of shikimate dehydrogenase .
Singh S, Korolev S, Koroleva O, Zarembinski T, Collart F, Joachimiak A, Christendat D; , J Biol Chem 2005;280:17101-17108.: Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae. PUBMED:15735308 EPMC:15735308
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013708
This domain is the substrate binding domain of shikimate dehydrogenase [PUBMED:15735308]. Shikimate dehydrogenase catalyses the fourth step of the mycobacterial Shikimate pathway, which results in the biosynthesis of chorismate. Chorismate is a precursor of aromatic amino acids, naphthoquinones, menaquinones and mycobactins [PUBMED:18260104, PUBMED:12637497]. This pathway is an important target for antibacterial agents, especially against Mycobacterium tuberculosis, since it does not occur in mammals.
|Molecular function||shikimate 3-dehydrogenase (NADP+) activity (GO:0004764)|
|Biological process||oxidation-reduction process (GO:0055114)|
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According to SCOP this superfamilies core fold has 3 layers in an alpha/beta/alpha configuration. Its central parallel beta sheet of four stands has the order 2134. In amino acid dehydrogenases this domain participates in dimerisation. This superfamily also includes domains from tetrahydrofolate dehydrogenase/cyclohydrolase, methylene-tetrahydromethanopterin dehydrogenase and shikimate dehydrogenase.
The clan contains the following 5 members:ELFV_dehydrog_N malic Mpt_N Shikimate_dh_N THF_DHG_CYH
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_99 (release 18.0)|
|Number in seed:||37|
|Number in full:||6188|
|Average length of the domain:||81.90 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||19.75 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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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 Shikimate_dh_N domain has been found. There are 113 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 seqence.
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