JmjCA domain family that is part of the cupin metalloenzyme superfamily.
|SMART accession number:||SM00558|
|Description:||Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).|
|Interpro abstract (IPR003347):|
The JmjN and JmjC domains are two non-adjacent domains which have been identified in the jumonji family of transcription factors. Although it was originally suggested that the JmjN and JmjC domains always co-occur and might form a single functional unit within the folded protein, the JmjC domain was latter found without the JmjN domain in organisms from bacteria to human [(PUBMED:10838566), (PUBMED:11165500)].
Proteins containing JmjC domain are predicted to be metalloenzymes that adopt the cupin fold and are candidates for enzymes that regulate chromatin remodelling [(PUBMED:11165500)]. The cupin fold is a flattened beta-barrel structure containing two sheets of five antiparallel beta strands that form the walls of a zinc-binding cleft. Based on the crystal structure of JmjC domain containing protein FIH and JHDM3A/JMJD2A, the JmjC domain forms an enzymatically active pocket that coordinates Fe(III) and alphaKG. Three amino-acid residues within the JmjC domain bind to the Fe(II) cofactor and two additional residues bind to alphaKG [(PUBMED:16983801)].
JmjC domains were identified in numerous eukaryotic proteins containing domains typical of transcription factors, such as PHD, C2H2, ARID/BRIGHT and zinc fingers [(PUBMED:11165500), (PUBMED:12446723)]. The JmjC has been shown to function in a histone demethylation mechanism that is conserved from yeast to human [(PUBMED:16362057)]. JmjC domain proteins may be protein hydroxylases that catalyse a novel histone modification [(PUBMED:15809658)]. The human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [(PUBMED:20739293)].
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- Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing JmjC domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with JmjC domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing JmjC domain in the selected taxonomic class.
- Literature (relevant references for this domain)
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 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 domain 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 FACTOR INHIBITING HIF-1 ALPHA WITH PYRIDINE 2,4 DICARBOXYLIC ACID 2w2i Crystal structure of the human 2-oxoglutarate oxygenase LOC390245 2wa3 FACTOR INHIBITING HIF-1 ALPHA WITH 2-(3-hydroxyphenyl)-2-oxoacetic acid 2wa4 FACTOR INHIBITING HIF-1 ALPHA WITH N,3-dihydroxybenzamide 2wwj STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A 2wwu Crystal structure of the catalytic domain of PHD finger protein 8 2xdv Crystal Structure of the Catalytic Domain of FLJ14393 2xml Crystal structure of human JMJD2C catalytic domain 2xue CRYSTAL STRUCTURE OF JMJD3 2xum FACTOR INHIBITING HIF (FIH) Q239H MUTANT IN COMPLEX WITH ZN(II), NOG AND ASP-SUBSTRATE PEPTIDE (20-MER) 2xxz Crystal structure of the human JMJD3 jumonji domain 2y0i FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH TANKYRASE-2 (TNKS2) FRAGMENT PEPTIDE (21-MER) 2ybk JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE 2ybp JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) 2ybs JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) 2yc0 FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE 2yde FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH S-2-HYDROXYGLUTARATE 2ypd Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein 2yu1 Crystal structure of hJHDM1A complexed with a-ketoglutarate 2yu2 Crystal structure of hJHDM1A without a-ketoglutarate 3al5 Crystal structure of Human TYW5 3al6 Crystal structure of Human TYW5 3avr Catalytic fragment of UTX/KDM6A bound with histone H3K27me3 peptide, N-oxyalylglycine, and Ni(II) 3avs Catalytic fragment of UTX/KDM6A bound with N-oxyalylglycine, and Ni(II) 3d8c Factor inhibiting HIF-1 alpha D201G mutant in complex with ZN(II), alpha-ketoglutarate and HIF-1 alpha 19mer 3dxt Crystal structure of the catalytic core domain of JMJD2D 3dxu The crystal structure of core JMJD2D complexed with FE and N-oxalylglycine 3k2o Structure of an oxygenase 3k3n Crystal structure of the catalytic core domain of human PHF8 3k3o Crystal structure of the catalytic core domain of human PHF8 complexed with alpha-ketoglutarate 3kcx Factor inhibiting HIF-1 alpha in complex with Clioquinol 3kcy Factor inhibiting HIF-1 alpha in complex with 8-hydroxyquinoline 3kv4 Structure of PHF8 in complex with histone H3 3kv5 Structure of KIAA1718, human Jumonji demethylase, in complex with N-oxalylglycine 3kv6 Structure of KIAA1718, human Jumonji demethylase, in complex with alpha-ketoglutarate 3kv9 Structure of KIAA1718 Jumonji domain 3kva Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate 3kvb Structure of KIAA1718 Jumonji domain in complex with N-oxalylglycine 3ld8 Structure of JMJD6 and Fab Fragments 3ldb Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment. 3n9l ceKDM7A from C.elegans, complex with H3K4me3 peptide and NOG 3n9m ceKDM7A from C.elegans, alone 3n9n ceKDM7A from C.elegans, complex with H3K4me3K9me2 peptide and NOG 3n9o ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K9me2 peptide and NOG 3n9p ceKDM7A from C.elegans, complex with H3K4me3K27me2 peptide and NOG 3n9q ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG 3njy Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyquinoline 3od4 Crystal Structure of Factor Inhibiting HIF-1 Alpha Complexed with Inhibitor 3opt Crystal structure of the Rph1 catalytic core with a-ketoglutarate 3opw Crystal Structure of the Rph1 catalytic core 3p3n Factor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mouse notch (1930-1949) peptide 3p3p Factor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mouse notch (1997-2016) peptide 3pdq Crystal structure of JMJD2A complexed with bipyridyl inhibitor 3ptr PHF2 Jumonji domain 3pu3 PHF2 Jumonji domain-NOG complex 3pu8 PHF2 Jumonji-NOG-Fe(II) complex 3pua PHF2 Jumonji-NOG-Ni(II) 3puq CEKDM7A from C.Elegans, complex with alpha-KG 3pur CEKDM7A from C.Elegans, complex with D-2-HG 3pus PHF2 Jumonji-NOG-Ni(II) 3rvh Crystal Structure of JMJD2A Complexed with Inhibitor 3u4s Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine 3u78 E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 Jumonji demethylase 3uyj Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG 3zli Crystal structure of JmjC domain of human histone demethylase UTY 3zpo Crystal structure of JmjC domain of human histone demethylase UTY with bound GSK J1 4aap Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG) 4ai8 FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH DAMINOZIDE 4ai9 JMJD2A COMPLEXED WITH DAMINOZIDE 4ask CRYSTAL STRUCTURE OF JMJD3 WITH GSK-J1 4b7e FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH CONSENSUS ANKYRIN REPEAT DOMAIN-LEU PEPTIDE (20-MER) 4b7k FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH CONSENSUS ANKYRIN REPEAT DOMAIN-SER PEPTIDE (20-MER) 4bio FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH 8-HYDROXYQUINOLINE-5- CARBOXYLIC ACID 4bis JMJD2A COMPLEXED WITH 8-HYDROXYQUINOLINE-4-CARBOXYLIC ACID 4bu2 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG) 4c8d Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B) 4ccj 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form 4cck 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG) 4ccl X-Ray structure of E. coli ycfD 4ccm 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1) 4ccn 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2) 4cco 60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3) 4csw Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase 4cug Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment 4diq Crystal Structure of human NO66 4do0 Crystal Structure of human PHF8 in complex with Daminozide 4e4h Crystal structure of Histone Demethylase NO66 4eyu The free structure of the mouse C-terminal domain of KDM6B 4ez4 free KDM6B structure 4ezh the crystal structure of KDM6B bound with H3K27me3 peptide 4gaz Crystal Structure of a Jumonji Domain-containing Protein JMJD5 4gd4 Crystal Structure of JMJD2A Complexed with Inhibitor 4gjy JMJD5 in complex with N-Oxalylglycine 4gjz JMJD5 in complex with 2-oxoglutarate 4hon Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate 4hoo Crystal structure of human JMJD2D/KDM4D apoenzyme 4igo Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG 4igp Histone H3 Lysine 4 Demethylating Rice JMJ703 apo enzyme 4igq Histone H3 Lysine 4 Demethylating Rice JMJ703 in complex with methylated H3K4 substrate 4jaa Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)LEU peptide 4lit Structure of YcfD a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and 2-oxoglutarate. 4liu Structure of YcfD, a Ribosomal oxygenase from Escherichia coli. 4liv Structure of YcfD, a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and succinic acid. 4nub Crystal structure of Escherichia coli ribosomal oxygenase YcfD
- Links (links to other resources describing this domain)