Summary: Malic enzyme, N-terminal domain
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Malic enzyme, N-terminal domain Provide feedback
No Pfam abstract.
External database links
PRINTS: | PR00072 |
PROSITE: | PDOC00294 |
SCOP: | 1qr6 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR012301
Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate, a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis [PUBMED:8300616]. There are 3 forms of the enzyme [PUBMED:1993674]: an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form [PUBMED:8300616]. Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase [PUBMED:2103472]; and the hypothetical Saccharomyces cerevisiae protein YKL029c.
Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity [PUBMED:1911848]. The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate-or divalent metal ion-binding in the active site [PUBMED:1911848]. Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme [PUBMED:1911848], although it is absent in the sequences from some species.
There are three well conserved regions in the enzyme sequences. Two of them seem to be involved in the binding NAD or NADP. The significance of the third one, located in the central part of the enzymes, is not yet known.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471) |
Biological process | oxidation-reduction process (GO:0055114) |
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 AA_dh_N (CL0603), which has the following description:
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_CYHAlignments
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 (48) |
Full (13950) |
Representative proteomes | UniProt (52631) |
NCBI (69491) |
Meta (2163) |
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RP15 (1638) |
RP35 (6361) |
RP55 (12997) |
RP75 (22041) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (48) |
Full (13950) |
Representative proteomes | UniProt (52631) |
NCBI (69491) |
Meta (2163) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1638) |
RP35 (6361) |
RP55 (12997) |
RP75 (22041) |
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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: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 48 |
Number in full: | 13950 |
Average length of the domain: | 138.90 aa |
Average identity of full alignment: | 37 % |
Average coverage of the sequence by the domain: | 26.22 % |
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: | 182 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 malic domain has been found. There are 108 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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