Summary: Heavy-metal-associated domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "HMA domain". More...
HMA domain Edit Wikipedia article
Heavy-metal-associated domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() solution structure of the n-terminal domain of znta in the zn(ii)-form
|
|||||||||
Identifiers | |||||||||
Symbol | HMA | ||||||||
Pfam | PF00403 | ||||||||
InterPro | IPR006121 | ||||||||
PROSITE | PDOC00804 | ||||||||
SCOP | 2hqi | ||||||||
SUPERFAMILY | 2hqi | ||||||||
TCDB | 9.A.2 | ||||||||
|
In molecular biology, the HMA domain (heavy-metal-associated domain) is a conserved protein domain found in a number of heavy metal transport or detoxification proteins.[1]
Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases.[1]
The HMA domain, contains two conserved cysteines that are probably involved in metal binding. The fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold.[2] This fold is common to other domains and is classified as "ferredoxin-like".
References
- ^ a b Bull PC, Cox DW (July 1994). "Wilson disease and Menkes disease: new handles on heavy-metal transport". Trends Genet. 10 (7): 246–52. doi:10.1016/0168-9525(94)90172-4. PMID 8091505.
- ^ Gitschier J, Moffat B, Reilly D, Wood WI, Fairbrother WJ (January 1998). "Solution structure of the fourth metal-binding domain from the Menkes copper-transporting ATPase". Nat. Struct. Biol. 5 (1): 47–54. doi:10.1038/nsb0198-47. PMID 9437429.
This article incorporates text from the public domain Pfam and InterPro IPR006121
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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.
Heavy-metal-associated domain Provide feedback
No Pfam abstract.
Literature references
-
Rosenzweig AC, Huffman DL, Hou MY, Wernimont AK, Pufahl RA, O'Halloran TV; , Structure Fold Des 1999;7:605-617.: Crystal structure of the Atx1 metallochaperone protein at 1.02 A resolution. PUBMED:10404590 EPMC:10404590
Internal database links
SCOOP: | BUD22 Hydrolase RR_TM4-6 TusA |
External database links
HOMSTRAD: | HMA |
PROSITE: | PDOC00804 |
SCOP: | 2hqi |
Transporter classification: | 9.A.2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006121
Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures.
These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases [PUBMED:8091505].
A conserved domain has been found in a number of these heavy metal transport or detoxification proteins [PUBMED:8091505]. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding.
Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold [PUBMED:9437429]. This fold is common to other domains and is classified as "ferredoxin-like".
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | metal ion binding (GO:0046872) |
Biological process | metal ion transport (GO:0030001) |
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (48) |
Full (43600) |
Representative proteomes | UniProt (142575) |
NCBI (210123) |
Meta (1497) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (3682) |
RP35 (16037) |
RP55 (30628) |
RP75 (48421) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (48) |
Full (43600) |
Representative proteomes | UniProt (142575) |
NCBI (210123) |
Meta (1497) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (3682) |
RP35 (16037) |
RP55 (30628) |
RP75 (48421) |
||||||
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: | 43600 |
Average length of the domain: | 60.70 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 17.13 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 62 | ||||||||||||
Family (HMM) version: | 27 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
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...
Tree controls
HideThe 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.
Interactions
There are 6 interactions for this family. More...
Hydrolase E1-E2_ATPase Sod_Cu HMA Cation_ATPase_N Sod_CuStructures
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 HMA domain has been found. There are 183 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...