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192  structures 551  species 0  interactions 22165  sequences 264  architectures

Family: Hemopexin (PF00045)

Summary: Hemopexin

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 "Hemopexin family". More...

Hemopexin family Edit Wikipedia article

Hemopexin
Identifiers
SymbolHemopexin
PfamPF00045
InterProIPR000585
SMARTHX
PROSITEPDOC00023
SCOPe1hxn / SUPFAM
Membranome536

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

Human gene encoding proteins containing hemopexin-like repeats include:

References

  1. ^ Bode W (June 1995). "A helping hand for collagenases: the haemopexin-like domain". Structure. 3 (6): 527–30. doi:10.1016/s0969-2126(01)00185-x. 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


Internal database links

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).

The hemopexin domain exhibits the shape of an oblate ellipsoidal disk. The polypeptide chain is organised in four beta-sheet (blades) I to IV, which are almost symmetrically arranged around a central axis in consecutive order, giving rise to the formation of a four-bladed propeller. Each propeller blade or repeat is made up of four antiparallel beta-strands connected in a W-like strand topology, and is strongly twisted [ PUBMED:8969305 , PUBMED:20147493 ].

This entry represents the repeats found in hemopexin 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(22165)
Representative proteomes UniProt
(36799)
RP15
(2081)
RP35
(6842)
RP55
(18656)
RP75
(25202)
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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
(76)
Full
(22165)
Representative proteomes UniProt
(36799)
RP15
(2081)
RP35
(6842)
RP55
(18656)
RP75
(25202)
Alignment:
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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
(22165)
Representative proteomes UniProt
(36799)
RP15
(2081)
RP35
(6842)
RP55
(18656)
RP75
(25202)
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: SMART
Previous IDs: hemopexin;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Ponting CP , Bateman A , Sonnhammer ELL
Number in seed: 76
Number in full: 22165
Average length of the domain: 44.90 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 25.16 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 45
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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 192 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.

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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
A0A0N9E2K8 View 3D Structure Click here
A0A0N9E2K8 View 3D Structure Click here
A0A0R4IB00 View 3D Structure Click here
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A0A286Y9P6 View 3D Structure Click here
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A0A286YB36 View 3D Structure Click here
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A0A2R8Q2M8 View 3D Structure Click here
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A0A2R8RUJ1 View 3D Structure Click here
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A1EC81 View 3D Structure Click here
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B0R0I1 View 3D Structure Click here
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D3ZZ42 View 3D Structure Click here
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F1QC76 View 3D Structure Click here
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F1RA45 View 3D Structure Click here
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P57748 View 3D Structure Click here
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Q02853 View 3D Structure Click here
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Q10739 View 3D Structure Click here
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Q99PW6 View 3D Structure Click here
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Q9H239 View 3D Structure Click here
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Q9H306 View 3D Structure Click here
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