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96  structures 208  species 4  interactions 5321  sequences 87  architectures

Family: Hemopexin (PF00045)

Summary: Hemopexin

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This is the Wikipedia entry entitled "Hemopexin family". More...

Hemopexin family Edit Wikipedia article

Hemopexin
Identifiers
Symbol Hemopexin
Pfam PF00045
InterPro IPR000585
SMART HX
PROSITE PDOC00023
SCOP 1hxn
SUPERFAMILY 1hxn

The hemopexin family is a family of evolutionarily related proteins. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins).[1] The HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs).

Hemopexin (EC 3.2.1.35) is a serum glycoprotein that binds haem and transports it to the liver for breakdown and iron recovery, after which the free hemopexin returns to the circulation.[2] Hemopexin prevents haem-mediated oxidative stress. Structurally hemopexin consists of two similar halves of approximately two hundred amino acid residues connected by a histidine-rich hinge region. Each half is itself formed by the repetition of a basic unit of some 35 to 45 residues. Hemopexin-like domains have been found in two other types of proteins, vitronectin,[3] a cell adhesion and spreading factor found in plasma and tissues, and matrixins MMP-1, MMP-2, MMP-3, MMP-9, MMP-10, MMP-11, MMP-12, MMP-14, MMP-15 and MMP-16, members of the matrix metalloproteinase family that cleave extracellular matrix constituents.[4] These zinc endopeptidases, which belong to MEROPS peptidase subfamily M10A, have a single hemopexin-like domain in their C-terminal section. It is suggested that the hemopexin domain facilitates binding to a variety of molecules and proteins, for example the HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs).

Examples[edit]

Human gene encoding proteins containing hemopexin-like repeats include:

References[edit]

  1. ^ Bode W (June 1995). "A helping hand for collagenases: the haemopexin-like domain". Structure 3 (6): 527–30. PMID 8590012. 
  2. ^ Altruda F, Tolosano E (2002). "Hemopexin: structure, function, and regulation". DNA Cell Biol. 21 (4): 297–306. doi:10.1089/104454902753759717. PMID 12042069. 
  3. ^ Kojima K, Ogawa H, Matsumoto I, Yoneda A (1998). "Characterization of the ligand binding activities of vitronectin: interaction of vitronectin with lipids and identification of the binding domains for various ligands using recombinant domains". Biochemistry 37 (18): 6351–6360. doi:10.1021/bi972247n. PMID 9572850. 
  4. ^ Das S, Mandal M, Chakraborti T, Mandal A, Chakraborti S (2003). "Structure and evolutionary aspects of matrix metalloproteinases: a brief overview". Mol. Cell. Biochem. 253 (1–2): 31–40. doi:10.1023/A:1026093016148. PMID 14619953. 

This article incorporates text from the public domain Pfam and InterPro IPR000585

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.

Hemopexin Provide feedback

Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metallopeptidases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs).

Literature references

  1. Gomis-Ruth FX, Gohlke U, Betz M, Knauper V, Murphy G, Lopez-Otin C, Bode W , J Mol Biol 1996;264:556-566.: The helping hand of collagenase-3 (MMP-13): 2.7 A crystal structure of its C-terminal haemopexin-like domain. PUBMED:8969305 EPMC:8969305


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018487

Hemopexin (EC) is a serum glycoprotein that binds haem and transports it to the liver for breakdown and iron recovery, after which the free hemopexin returns to the circulation [PUBMED:12042069]. Hemopexin prevents haem-mediated oxidative stress. Structurally hemopexin consists of two similar halves of approximately two hundred amino acid residues connected by a histidine-rich hinge region. Each half is itself formed by the repetition of a basic unit of some 35 to 45 residues. Hemopexin-like domains have been found in two other types of proteins, vitronectin [PUBMED:9572850], a cell adhesion and spreading factor found in plasma and tissues, and matrixins MMP-1, MMP-2, MMP-3, MMP-9, MMP-10, MMP-11, MMP-12, MMP-14, MMP-15 and MMP-16, members of the matrix metalloproteinase family that cleave extracellular matrix constituents [PUBMED:14619953]. These zinc endopeptidases, which belong to MEROPS peptidase subfamily M10A, have a single hemopexin-like domain in their C-terminal section. It is suggested that the hemopexin domain facilitates binding to a variety of molecules and proteins, for example the HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs).

This entry represents the repeat found in hempoxein and related domains.

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
(76)
Full
(5321)
Representative proteomes NCBI
(4600)
Meta
(17)
RP15
(348)
RP35
(533)
RP55
(1140)
RP75
(2483)
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Format an alignment

  Seed
(76)
Full
(5321)
Representative proteomes NCBI
(4600)
Meta
(17)
RP15
(348)
RP35
(533)
RP55
(1140)
RP75
(2483)
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
(76)
Full
(5321)
Representative proteomes NCBI
(4600)
Meta
(17)
RP15
(348)
RP35
(533)
RP55
(1140)
RP75
(2483)
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.

Pfam alignments:

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: SMART
Previous IDs: hemopexin;
Type: Repeat
Author: Ponting C, Bateman A, Sonnhammer ELL
Number in seed: 76
Number in full: 5321
Average length of the domain: 44.70 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 26.74 %

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 21.3 21.3
Trusted cut-off 21.5 21.3
Noise cut-off 21.1 21.2
Model length: 45
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 4 interactions for this family. More...

PG_binding_1 Peptidase_M10 Hemopexin fn2

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 Hemopexin domain has been found. There are 96 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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