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7  structures 2461  species 1  interaction 2836  sequences 25  architectures

Family: AMMECR1 (PF01871)

Summary: AMMECR1

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AMMECR1 Edit Wikipedia article

AMMECR1
PDB 1zq7 EBI.jpg
X-ray crystal structure of protein q8pzk8 from methanosarcina mazei. northeast structural genomics consortium target mar9.
Identifiers
Symbol AMMECR1
Pfam PF01871
InterPro IPR002733

In molecular biology, the AMMECR1 protein (Alport syndrome, intellectual disability, midface hypoplasia and elliptocytosis chromosomal region gene 1 protein) is a protein encoded by the AMMECR1 gene on human chromosome Xq22.3.

The contiguous gene deletion syndrome is characterised by Alport syndrome (A), intellectual disability (M), midface hypoplasia (M), and elliptocytosis (E), as well as generalized hypoplasia and cardiac abnormalities. It is caused by a deletion in Xq22.3, comprising several genes including AMME chromosomal region gene 1 (AMMECR1), which encodes a protein with a nuclear location and presently unknown function. The C-terminal region of AMMECR1 (from residue 122 to 333) is well conserved, and homologues appear in species ranging from bacteria and archaea to eukaryotes. The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery.[1][2]

The AMMECR1 domain contains a six-amino-acid motif (LRGCIG) that might be functionally important since it is strikingly conserved throughout evolution.[1] The AMMECR1 domain consists of two distinct subdomains of different sizes. The large subdomain, which contains both the N- and C-terminal regions, consists of five alpha-helices and five beta-strands. These five beta-strands form an antiparallel beta-sheet. The small subdomain consists of four alpha-helices and three beta-strands, and these beta-strands also form an antiparallel beta-sheet. The conserved 'LRGCIG' motif is located at beta(2) and its N-terminal loop, and most of the side chains of these residues point toward the interface of the two subdomains. The two subdomains are connected by only two loops, and the interaction between the two subdomains is not strong. Thus, these subdomains may move dynamically when the substrate enters the cleft. The size of the cleft suggests that the substrate is large, e.g., the substrate may be a nucleic acid or protein. However, the inner side of the cleft is not filled with positively charged residues, and therefore it is unlikely that negatively charged nucleic acids such as DNA or RNA interact at this site.[3]

References

  1. ^ a b Vitelli F, Piccini M, Caroli F, Franco B, Malandrini A, Pober B, Jonsson J, Sorrentino V, Renieri A (February 1999). "Identification and characterization of a highly conserved protein absent in the Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E) contiguous gene deletion syndrome (AMME)". Genomics. 55 (3): 335–40. doi:10.1006/geno.1998.5666. PMID 10049589. 
  2. ^ Vitelli F, Meloni I, Fineschi S, Favara F, Tiziana Storlazzi C, Rocchi M, Renieri A (2000). "Identification and characterization of mouse orthologs of the AMMECR1 and FACL4 genes deleted in AMME syndrome: orthology of Xq22.3 and MmuXF1-F3". Cytogenet. Cell Genet. 88 (3-4): 259–63. doi:10.1159/000015533. PMID 10828604. 
  3. ^ Tajika Y, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I (February 2005). "Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region". Proteins. 58 (2): 501–3. doi:10.1002/prot.20315. PMID 15558565. 

This article incorporates text from the public domain Pfam and InterPro IPR002733

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This family consists of several AMMECR1 as well as several uncharacterised proteins. The contiguous gene deletion syndrome AMME is characterised by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1 [1]. This family contains sequences from several eukaryotic species as well as archaebacteria and it has been suggested that the AMMECR1 protein may have a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [2].

Literature references

  1. Vitelli F, Meloni I, Fineschi S, Favara F, Tiziana Storlazzi C, Rocchi M, Renieri A; , Cytogenet Cell Genet 2000;88:259-263.: Identification and characterization of mouse orthologs of the AMMECR1 and FACL4 genes deleted in AMME syndrome: orthology of Xq22.3 and MmuXF1-F3. PUBMED:10828604 EPMC:10828604

  2. Vitelli F, Piccini M, Caroli F, Franco B, Malandrini A, Pober B, Jonsson J, Sorrentino V, Renieri A; , Genomics 1999;55:335-340.: Identification and characterization of a highly conserved protein absent in the Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E) contiguous gene deletion syndrome (AMME). PUBMED:10049589 EPMC:10049589


This tab holds annotation information from the InterPro database.

InterPro entry IPR002733

The contiguous gene deletion syndrome is characterised by Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E), as well as generalized hypoplasia and cardiac abnormalities. It is caused by a deletion in Xq22.3, comprising several genes including AMME chromosomal region gene 1 (AMMECR1), which encodes a protein with a nuclear location and presently unknown function. The C-terminal region of AMMECR1 (from residue 122 to 333) is well conserved, and homologues appear in species ranging from bacteria and archaea to eukaryotes. The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [PUBMED:10049589, PUBMED:10828604].

The AMMECR1 domain contains a 6-amino-acid motif (LRGCIG) that might be functionally important since it is strikingly conserved throughout evolution [PUBMED:10049589]. The AMMECR1 domain consists of two distinct subdomains of different sizes. The large subdomain, which contains both the N- and C-terminal regions, consists of five alpha-helices and five beta-strands. These five beta-strands form an antiparallel beta-sheet. The small subdomain consists of four alpha-helices and three beta-strands, and these beta-strands also form an antiparallel beta-sheet. The conserved 'LRGCIG' motif is located at beta(2) and its N-terminal loop, and most of the side chains of these residues point toward the interface of the two subdomains. The two subdomains are connected by only two loops, and the interaction between the two subdomains is not strong. Thus, these subdomains may move dynamically when the substrate enters the cleft. The size of the cleft suggests that the substrate is large, e.g., the substrate may be a nucleic acid or protein. However, the inner side of the cleft is not filled with positively charged residues, and therefore it is unlikely that negatively charged nucleic acids such as DNA or RNA interact at this site [PUBMED:15558565].

Domain organisation

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Alignments

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  Seed
(377)
Full
(2836)
Representative proteomes UniProt
(6062)
NCBI
(6525)
Meta
(86)
RP15
(1041)
RP35
(2005)
RP55
(2740)
RP75
(3348)
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  Seed
(377)
Full
(2836)
Representative proteomes UniProt
(6062)
NCBI
(6525)
Meta
(86)
RP15
(1041)
RP35
(2005)
RP55
(2740)
RP75
(3348)
Alignment:
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  Seed
(377)
Full
(2836)
Representative proteomes UniProt
(6062)
NCBI
(6525)
Meta
(86)
RP15
(1041)
RP35
(2005)
RP55
(2740)
RP75
(3348)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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Curation and family details

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Seed source: Enright A
Previous IDs: DUF51;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A , Moxon SJ
Number in seed: 377
Number in full: 2836
Average length of the domain: 172.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 61.89 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.2 25.0
Noise cut-off 21.9 21.7
Model length: 166
Family (HMM) version: 17
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Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There is 1 interaction for this family. More...

AMMECR1

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 AMMECR1 domain has been found. There are 7 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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