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HMA, heavy metal-associated domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   HMA, heavy metal-associated domain [ 55008]
Families:   HMA, heavy metal-associated domain [ 55009] (8)


Superfamily statistics
Genomes (2,751) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 19,000 82,521 21
Proteins 14,380 64,548 20


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.0033770.08421Least InformativeInherited
Biological Process (BP)single-organism cellular process0.15381Least InformativeInherited
Biological Process (BP)ion transport0.00011430Moderately InformativeDirect
Biological Process (BP)regulation of biological quality0.00000086420.0000000001356Moderately InformativeDirect
Biological Process (BP)cation homeostasis0.0000000000064480InformativeDirect
Biological Process (BP)inorganic ion homeostasis0.0000000000067270InformativeDirect
Biological Process (BP)metal ion transport00.001139InformativeInherited
Biological Process (BP)transition metal ion transport00Highly InformativeDirect
Biological Process (BP)transition metal ion homeostasis00.0000000000001387Highly InformativeDirect
Molecular Function (MF)binding0.0018380.01501Least InformativeInherited
Molecular Function (MF)metal ion binding0.0000000056890Moderately InformativeDirect
Molecular Function (MF)copper ion binding0.0000000000000013860Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0.0005131 Least Informative Direct
Biological Process (BP) biological regulation 0.08421 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) ion transport 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.0000000001356 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.3272 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.4796 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) response to metal ion 0 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) inorganic ion homeostasis 0 Informative Direct
Biological Process (BP) transmembrane transport 0.08908 Informative Inherited
Biological Process (BP) response to oxidative stress 0.001135 Informative Inherited
Biological Process (BP) intracellular transport 1 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0.09478 Informative Inherited
Biological Process (BP) metal ion transport 0.001139 Informative Inherited
Biological Process (BP) transition metal ion transport 0 Highly Informative Direct
Biological Process (BP) pigmentation 0.000003554 Highly Informative Direct
Biological Process (BP) response to copper ion 0.0000007773 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.0000000000001387 Highly Informative Direct
Biological Process (BP) inorganic cation transmembrane transport 0.0000000929 Highly Informative Direct
Biological Process (BP) detoxification 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.1333 Least Informative Inherited
Molecular Function (MF) binding 0.01501 Least Informative Inherited
Molecular Function (MF) transporter activity 0.000000003549 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00002057 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.002399 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 0.000001687 Informative Direct
Molecular Function (MF) P-P-bond-hydrolysis-driven transmembrane transporter activity 0.00000000001001 Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 0.000000000005985 Informative Direct
Molecular Function (MF) ATPase activity 0.0000002085 Informative Direct
Molecular Function (MF) active ion transmembrane transporter activity 0.0000003372 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Molecular Function (MF) ATPase coupled ion transmembrane transporter activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.004578 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.07985 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.04764 Least Informative Inherited
Cellular Component (CC) membrane 0.002713 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.00181 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.07865 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.0000000007668 Informative Direct
Cellular Component (CC) endosome 0.03403 Informative Inherited
Cellular Component (CC) late endosome 0.0006796 Highly Informative Direct
Cellular Component (CC) cell-cell junction 0.00006207 Highly Informative Direct
Cellular Component (CC) symplast 0.000000991 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.3102Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembran0InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0InformativeDirect
Enzyme Commission (EC)Copper-exporting ATPase0Highly InformativeDirect
Enzyme Commission (EC)Mercury(II) reductase0Highly InformativeDirect
Enzyme Commission (EC)Cu(+) exporting ATPase0Highly InformativeDirect
Enzyme Commission (EC)Cadmium-exporting ATPase0Highly InformativeDirect
Enzyme Commission (EC)Zinc-exporting ATPase0.000000000000008737Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0.000002407Moderately InformativeDirect
Cellular componentCell membrane0.000003089Moderately InformativeDirect
Cellular componentPeriplasm0.000002975InformativeDirect
DomainTransmembrane0.000000000000003069Least InformativeDirect
DomainRedox-active center0.0000005527InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0.000000000005241Least InformativeDirect
Molecular functionNucleotide-binding0.548Least InformativeInherited
Molecular functionZinc1Least InformativeInherited
Molecular functionFlavoprotein0.06157Moderately InformativeInherited
Molecular functionCopper0InformativeDirect
Molecular functionFAD0.00002225InformativeDirect
Molecular functionCadmium0Highly InformativeDirect
Molecular functionMercury0Highly InformativeDirect
Molecular functionZinc transport0.000000008007Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationMethylation0.00000000002784Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006121 SSF55008 Protein matches
Abstract

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 [PubMed8091505].

A conserved domain has been found in a number of these heavy metal transport or detoxification proteins [PubMed8091505]. 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 [PubMed9437429]. This fold is common to other domains and is classified as "ferredoxin-like".


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 15 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a HMA, heavy metal-associated domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 15 hidden Markov models representing the HMA, heavy metal-associated domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]