Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
778  structures 1440  species 0  interactions 16909  sequences 433  architectures

Family: JmjC (PF02373)

Summary: JmjC domain, hydroxylase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

JmjC domain, hydroxylase Provide feedback

The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].

Literature references

  1. Balciunas D, Ronne H; , Trends Biochem Sci 2000;25:274-276.: Evidence of domain swapping within the jumonji family of transcription factors. PUBMED:10838566 EPMC:10838566

  2. Ayoub N, Noma K, Isaac S, Kahan T, Grewal SI, Cohen A; , Mol Cell Biol 2003;23:4356-4370.: A novel jmjC domain protein modulates heterochromatization in fission yeast. PUBMED:12773576 EPMC:12773576

  3. Clissold PM, Ponting CP; , Trends Biochem Sci 2001;26:7-9.: JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta. PUBMED:11165500 EPMC:11165500

  4. Trewick SC, McLaughlin PJ, Allshire RC; , EMBO Rep 2005;6:315-320.: Methylation: lost in hydroxylation?. PUBMED:15809658 EPMC:15809658

  5. Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T;, J Biol Chem. 2010;285:34503-34507.: Expanding role of the jumonji C domain as an RNA hydroxylase. PUBMED:20739293 EPMC:20739293


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry 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 later 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 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

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 and the UniProtKB sequence database. More...

View options

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
(30)
Full
(16909)
Representative proteomes UniProt
(29188)
RP15
(2363)
RP35
(6841)
RP55
(13639)
RP75
(18672)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(30)
Full
(16909)
Representative proteomes UniProt
(29188)
RP15
(2363)
RP35
(6841)
RP55
(13639)
RP75
(18672)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(30)
Full
(16909)
Representative proteomes UniProt
(29188)
RP15
(2363)
RP35
(6841)
RP55
(13639)
RP75
(18672)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: [1]
Previous IDs: jmjC;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Wood V , Mistry J
Number in seed: 30
Number in full: 16909
Average length of the domain: 109.70 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 9.91 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 114
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 JmjC domain has been found. There are 778 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.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JTU9 View 3D Structure Click here
A0A0G2K5I7 View 3D Structure Click here
A0A0G2K6D0 View 3D Structure Click here
A0A0G2K6G9 View 3D Structure Click here
A0A0G2K897 View 3D Structure Click here
A0A0G2KAI2 View 3D Structure Click here
A0A0G2KR99 View 3D Structure Click here
A0A0P0V3U4 View 3D Structure Click here
A0A0P0VE06 View 3D Structure Click here
A0A0P0X1F1 View 3D Structure Click here
A0A0P0XMK7 View 3D Structure Click here
A0A0R0E4Q8 View 3D Structure Click here
A0A0R0ETQ4 View 3D Structure Click here
A0A0R0EVH9 View 3D Structure Click here
A0A0R0GD18 View 3D Structure Click here
A0A0R0GMN2 View 3D Structure Click here
A0A0R0I1P8 View 3D Structure Click here
A0A0R0IEN8 View 3D Structure Click here
A0A0R0J5F2 View 3D Structure Click here
A0A0R0JIN2 View 3D Structure Click here
A0A0R0L547 View 3D Structure Click here
A0A0R0L9F6 View 3D Structure Click here
A0A0R4IDZ5 View 3D Structure Click here
A0A0R4IYD2 View 3D Structure Click here
A0A131MBT2 View 3D Structure Click here
A0A131MD13 View 3D Structure Click here
A0A1D5NSI1 View 3D Structure Click here
A0A1D6FJ77 View 3D Structure Click here
A0A1D6FKW1 View 3D Structure Click here
A0A1D6G6Q6 View 3D Structure Click here
A0A1D6GT42 View 3D Structure Click here
A0A1D6GXC6 View 3D Structure Click here
A0A1D6HGP8 View 3D Structure Click here
A0A1D6HR86 View 3D Structure Click here
A0A1D6I3T4 View 3D Structure Click here
A0A1D6IVJ9 View 3D Structure Click here
A0A1D6IXA2 View 3D Structure Click here
A0A1D6K9X2 View 3D Structure Click here
A0A1D6KJ56 View 3D Structure Click here
A0A1D6KWN0 View 3D Structure Click here
A0A1D6LWC4 View 3D Structure Click here
A0A1D6M0J5 View 3D Structure Click here
A0A1D6N409 View 3D Structure Click here
A0A1D6PAE8 View 3D Structure Click here
A0A1D6PJW6 View 3D Structure Click here
A0A1D6QA82 View 3D Structure Click here
A0A1D6QB64 View 3D Structure Click here
A0A1D6QB77 View 3D Structure Click here
A0A1D6QBK5 View 3D Structure Click here
A0A1D8PDM2 View 3D Structure Click here
A0A1D8PDM2 View 3D Structure Click here
A0A1D8PL24 View 3D Structure Click here
A0A1D8PLL0 View 3D Structure Click here
A0A1D8PLN0 View 3D Structure Click here
A0A1P8AP94 View 3D Structure Click here
A0A1P8AUH1 View 3D Structure Click here
A0A1W2PPD8 View 3D Structure Click here
A0A2R8QCF1 View 3D Structure Click here
A0A2R8QIR8 View 3D Structure Click here
A0A2R8QNH2 View 3D Structure Click here
A0A2R8QQ41 View 3D Structure Click here
A0A368UHG7 View 3D Structure Click here
A0A368UI23 View 3D Structure Click here
A1A5Q5 View 3D Structure Click here
A1L1S9 View 3D Structure Click here
A4I2R6 View 3D Structure Click here
B0S6L0 View 3D Structure Click here
B2RXH2 View 3D Structure Click here
C0SUT9 View 3D Structure Click here
C0SV12 View 3D Structure Click here
D3ZJ51 View 3D Structure Click here
D4A029 View 3D Structure Click here
D4AD31 View 3D Structure Click here
E9QG91 View 3D Structure Click here
F1LMK8 View 3D Structure Click here
F1LS62 View 3D Structure Click here
F1Q597 View 3D Structure Click here
F1QNG0 View 3D Structure Click here
F1QPD2 View 3D Structure Click here
F4HZD1 View 3D Structure Click here
F4I6G4 View 3D Structure Click here
F4KIX0 View 3D Structure Click here
F6P9Q3 View 3D Structure Click here
G3V9U4 View 3D Structure Click here
I1JXF4 View 3D Structure Click here
I1JXF5 View 3D Structure Click here
I1KC81 View 3D Structure Click here
I1KQR1 View 3D Structure Click here
I1LBW9 View 3D Structure Click here
I1LCZ6 View 3D Structure Click here
I1MHR7 View 3D Structure Click here
I1MR29 View 3D Structure Click here
I1NHH0 View 3D Structure Click here
I3ITH4 View 3D Structure Click here
K7K577 View 3D Structure Click here
K7KQR0 View 3D Structure Click here
K7L2L5 View 3D Structure Click here
K7L3Y3 View 3D Structure Click here
K7L6B8 View 3D Structure Click here
K7LCJ5 View 3D Structure Click here
K7LF38 View 3D Structure Click here
K7LJJ4 View 3D Structure Click here
K7LKB6 View 3D Structure Click here
K7LLZ6 View 3D Structure Click here
K7LMP3 View 3D Structure Click here
K7LR91 View 3D Structure Click here
K7M1Q8 View 3D Structure Click here
K7MA03 View 3D Structure Click here
K7MAT1 View 3D Structure Click here
K7MYQ0 View 3D Structure Click here
K7N4Y4 View 3D Structure Click here
K7N597 View 3D Structure Click here
K7UT89 View 3D Structure Click here
M0RB75 View 3D Structure Click here
M0RBV7 View 3D Structure Click here
M0RDF1 View 3D Structure Click here
O13977 View 3D Structure Click here
O14607 View 3D Structure Click here
O15054 View 3D Structure Click here
O15550 View 3D Structure Click here
O43593 View 3D Structure Click here
O64752 View 3D Structure Click here
O70546 View 3D Structure Click here
O75151 View 3D Structure Click here
O75164 View 3D Structure Click here
O94603 View 3D Structure Click here
O94691 View 3D Structure Click here
O94953 View 3D Structure Click here
P0CF52 View 3D Structure Click here
P0CH95 View 3D Structure Click here
P29375 View 3D Structure Click here
P39956 View 3D Structure Click here
P41229 View 3D Structure Click here
P41230 View 3D Structure Click here
P47156 View 3D Structure Click here
P79457 View 3D Structure Click here
P97609 View 3D Structure Click here
Q03833 View 3D Structure Click here
Q0DJC2 View 3D Structure Click here
Q0DR01 View 3D Structure Click here
Q0DYF8 View 3D Structure Click here
Q10LJ3 View 3D Structure Click here
Q10RP4 View 3D Structure Click here
Q14V35 View 3D Structure Click here
Q15652 View 3D Structure Click here
Q19760 View 3D Structure Click here
Q1LUQ0 View 3D Structure Click here
Q1LVC2 View 3D Structure Click here
Q20367 View 3D Structure Click here
Q23541 View 3D Structure Click here
Q2QTX9 View 3D Structure Click here
Q336N8 View 3D Structure Click here
Q3U2K5 View 3D Structure Click here
Q3UWM4 View 3D Structure Click here
Q3UXZ9 View 3D Structure Click here
Q4CXU5 View 3D Structure Click here
Q4D046 View 3D Structure Click here
Q53WJ1 View 3D Structure Click here
Q55ER4 View 3D Structure Click here
Q5N712 View 3D Structure Click here
Q5NCY0 View 3D Structure Click here
Q5RHD1 View 3D Structure Click here
Q61645 View 3D Structure Click here
Q62240 View 3D Structure Click here
Q62315 View 3D Structure Click here
Q63679 View 3D Structure Click here
Q69ZK6 View 3D Structure Click here
Q6AYK2 View 3D Structure Click here
Q6B0I6 View 3D Structure Click here
Q6BDA0 View 3D Structure Click here
Q6IQX0 View 3D Structure Click here
Q6K7P0 View 3D Structure Click here
Q6NYC1 View 3D Structure Click here
Q6P949 View 3D Structure Click here
Q6PCM1 View 3D Structure Click here
Q6PFM0 View 3D Structure Click here
Q6ZMT4 View 3D Structure Click here
Q6ZPY7 View 3D Structure Click here
Q7LBC6 View 3D Structure Click here
Q80TJ7 View 3D Structure Click here
Q80Y84 View 3D Structure Click here
Q8BW72 View 3D Structure Click here
Q8GUI6 View 3D Structure Click here
Q8H1S7 View 3D Structure Click here
Q8IAT4 View 3D Structure Click here
Q8IAT4 View 3D Structure Click here
Q8L7T6 View 3D Structure Click here
Q8VCD7 View 3D Structure Click here
Q8VYB9 View 3D Structure Click here
Q91VY5 View 3D Structure Click here
Q92833 View 3D Structure Click here
Q95QK3 View 3D Structure Click here
Q9BY66 View 3D Structure Click here
Q9ERI5 View 3D Structure Click here
Q9GYI0 View 3D Structure Click here
Q9GYI4 View 3D Structure Click here
Q9H3R0 View 3D Structure Click here
Q9H9V9 View 3D Structure Click here
Q9HDV4 View 3D Structure Click here
Q9SSE9 View 3D Structure Click here
Q9STM3 View 3D Structure Click here
Q9U297 View 3D Structure Click here
Q9UGL1 View 3D Structure Click here
Q9UPP1 View 3D Structure Click here
Q9US53 View 3D Structure Click here
Q9UT79 View 3D Structure Click here
Q9V333 View 3D Structure Click here
Q9V6L0 View 3D Structure Click here
Q9VD28 View 3D Structure Click here
Q9VHC5 View 3D Structure Click here
Q9VJ97 View 3D Structure Click here
Q9VL07 View 3D Structure Click here
Q9VMJ7 View 3D Structure Click here
Q9VT00 View 3D Structure Click here
Q9WTU0 View 3D Structure Click here
Q9Y4C1 View 3D Structure Click here
W8C8J2 View 3D Structure Click here