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120  structures 4700  species 2  interactions 19664  sequences 116  architectures

Family: HMA (PF00403)

Summary: Heavy-metal-associated domain

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This is the Wikipedia entry entitled "HMA domain". More...

HMA domain Edit Wikipedia article

Heavy-metal-associated domain
PDB 1mwz EBI.jpg
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[edit]

  1. ^ 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. 
  2. ^ 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

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Literature references

  1. 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


External database links

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

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Domain organisation

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

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(73)
Full
(19664)
Representative proteomes NCBI
(15739)
Meta
(1631)
RP15
(1678)
RP35
(3706)
RP55
(5056)
RP75
(6028)
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Format an alignment

  Seed
(73)
Full
(19664)
Representative proteomes NCBI
(15739)
Meta
(1631)
RP15
(1678)
RP35
(3706)
RP55
(5056)
RP75
(6028)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(73)
Full
(19664)
Representative proteomes NCBI
(15739)
Meta
(1631)
RP15
(1678)
RP35
(3706)
RP55
(5056)
RP75
(6028)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD, Griffiths-Jones SR
Number in seed: 73
Number in full: 19664
Average length of the domain: 61.20 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 16.34 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 62
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

HMA Sod_Cu

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 HMA domain has been found. There are 120 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 seqence.

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