JmjCA domain family that is part of the cupin metalloenzyme superfamily. |
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| SMART accession number: | SM00558 |
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| Description: | Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press). |
| Interpro abstract (IPR003347): | This entry contains:
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| Family alignment: |
There are 1750 JmjC domains in 1750 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes - Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Balciunas D, Ronne H
- Evidence of domain swapping within the jumonji family of transcription factors.
- Trends Biochem Sci. 2000; 25: 274-6
- Dunwell JM, Khuri S, Gane PJ
- Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.
- Microbiol Mol Biol Rev. 2000; 64: 153-79
- Display abstract
This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.
- Ponting CP
- Evidence for PDZ domains in bacteria, yeast, and plants.
- Protein Sci. 1997; 6: 464-8
- Display abstract
Several dozen signaling proteins are now known to contain 80-100 residue repeats, called PDZ (or DHR or GLGF) domains, several of which interact with the C-terminal tetrapeptide motifs X-Ser/Thr-X-Val-COO- of ion channels and/or receptors. PDZ domains have previously been noted only in mammals, flies, and worms, suggesting that the primordial PDZ domain arose relatively late in eukaryotic evolution. Here, techniques of sequence analysis-including local alignment, profile, and motif database searches-indicate that PDZ domain homologues are present in yeast, plants, and bacteria. It is suggested that two PDZ domains occur in bacterial high-temperature requirement A (htrA) and one in tail-specific protease (tsp) homologues, and that a yeast htrA homologue contains four PDZ domains. Sequence comparisons suggest that the spread of PDZ domains in these diverse organisms may have occurred via horizontal gene transfer. The known affinity of Escherichia coli tsp for C-terminal polypeptides is proposed to be mediated by its PDZ-like domain, in a similar manner to the binding of C-terminal polypeptides by animal PDZ domains.
- Cleasby A et al.
- The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution.
- Nat Struct Biol. 1996; 3: 470-9
- Display abstract
Phosphomannose isomerase (PMI) catalyses the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P). Absence of PMI activity in yeasts causes cell lysis and thus the enzyme is a potential target for inhibition and may be a route to antifungal drugs. The 1.7 A crystal structure of PMI from Candida albicans shows that the enzyme has three distinct domains. The active site lies in the central domain, contains a single essential zinc atom, and forms a deep, open cavity of suitable dimensions to contain M6P or F6P The central domain is flanked by a helical domain on one side and a jelly-roll like domain on the other.
- Structure (3D structures containing this domain)
3D Structures of JmjC domains in PDB
PDB code Main view Title 1h2k 
Factor inhibiting hif-1 alpha in complex with hif-1 alpha fragment peptide 1h2l 
Factor inhibiting hif-1 alpha in complex with hif-1 alpha fragment peptide 1h2m 
Factor inhibiting hif-1 alpha in complex with hif-1 alpha fragment peptide 1h2n 
Factor inhibiting hif-1 alpha 1iz3 
Dimeric structure of fih (factor inhibiting hif) 1mze 
Human factor inhibiting hif (fih1) 1mzf 
Human factor inhibiting hif (fih1) in complex with 2- oxoglutarate 1vrb 
Crystal structure of putative asparaginyl hydroxylase (2636534) from bacillus subtilis at 2.60 a resolution 1yci 
Factor inhibiting hif-1 alpha in complex with n- (carboxycarbonyl)-d-phenylalanine 2cgn 
Factor inhibiting hif-1 alpha with succinate 2cgo 
Factor inhibiting hif-1 alpha with fumarate 2gp3 
Crystal structure of the catalytic core comain of jmjd2a 2gp5 
Crystal structure of catalytic core domain of jmjd2a complexed with alpha-ketoglutarate 2ilm 
Factor inhibiting hif-1 alpha d201a mutant in complex with fe(ii), alpha-ketoglutarate and hif-1 alpha 35mer 2oq6 
Crystal structure of jmjd2a complexed with histone h3 peptide trimethylated at lys9 2oq7 
The crystal structure of jmjd2a complexed with ni and n- oxalylglycine 2os2 
Crystal structure of jmjd2a complexed with histone h3 peptide trimethylated at lys36 2ot7 
Crystal structure of jmjd2a complexed with histone h3 peptide monomethylated at lys9 2ox0 
Crystal structure of jmjd2a complexed with histone h3 peptide dimethylated at lys9 2p5b 
The complex structure of jmjd2a and trimethylated h3k36 peptide 2pxj 
The complex structure of jmjd2a and monomethylated h3k36 peptide 2q8c 
Crystal structure of jmjd2a in ternary complex with an histone h3k9me3 peptide and 2-oxoglutarate 2q8d 
Crystal structure of jmj2d2a in ternary complex with histone h3-k36me2 and succinate 2q8e 
Specificity and mechanism of jmjd2a, a trimethyllysine- specific histone demethylase 2vd7 
Crystal structure of jmjd2a complexed with inhibitor pyridine-2,4-dicarboxylic acid 2w0x 
2w2i 
2wwu 
2yu1 
Crystal structure of hjhdm1a complexed with a-ketoglutarate 2yu2 
Crystal structure of hjhdm1a without a-ketoglutarate 3d8c 
Factor inhibiting hif-1 alpha d201g mutant in complex with zn(ii), alpha-ketoglutarate and hif-1 alpha 19mer 3dxt 
3dxu 
3k2o 
- Links (links to other resources describing this domain)
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INTERPRO IPR003347
