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4  structures 2788  species 1  interaction 3330  sequences 11  architectures

Family: CRS1_YhbY (PF01985)

Summary: CRS1 / YhbY (CRM) domain

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CRM domain Edit Wikipedia article

CRS1_YhbY
PDB 1rq8 EBI.jpg
solution structure of the hypothetical protein sav1595 from staphylococcus aureus, a putative rna binding protein
Identifiers
Symbol CRS1_YhbY
Pfam PF01985
InterPro IPR001890
PROSITE PDOC01005
SCOP 1jo0
SUPERFAMILY 1jo0

In molecular biology, the CRM domain is an approximately 100-amino acid RNA-binding domain. The name CRM (chloroplast RNA splicing and ribosome maturation) has been suggested to reflect the functions established for four characterised members of the family: Zea mays (Maize) CRS1, CAF1 and CAF2 proteins and the Escherichia coli protein YhbY. Proteins containing the CRM domain are found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets.[1][2]

The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue.[3]

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants.[2] A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing.[4] In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes.[2] YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.[5]

References[edit]

  1. ^ Ostheimer GJ, Williams-Carrier R, Belcher S, Osborne E, Gierke J, Barkan A (August 2003). "Group II intron splicing factors derived by diversification of an ancient RNA-binding domain". EMBO J. 22 (15): 3919–29. doi:10.1093/emboj/cdg372. PMC 169045. PMID 12881426. 
  2. ^ a b c Barkan A, Klipcan L, Ostersetzer O, Kawamura T, Asakura Y, Watkins KP (January 2007). "The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein". RNA 13 (1): 55–64. doi:10.1261/rna.139607. PMC 1705760. PMID 17105995. 
  3. ^ Ostheimer GJ, Barkan A, Matthews BW (November 2002). "Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins". Structure 10 (11): 1593–601. doi:10.1016/S0969-2126(02)00886-9. PMID 12429100. 
  4. ^ Asakura Y, Barkan A (December 2007). "A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts". Plant Cell 19 (12): 3864–75. doi:10.1105/tpc.107.055160. PMC 2217638. PMID 18065687. 
  5. ^ Till B, Schmitz-Linneweber C, Williams-Carrier R, Barkan A (September 2001). "CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin". RNA 7 (9): 1227–38. doi:10.1017/S1355838201010445. PMC 1370168. PMID 11565746. 

This article incorporates text from the public domain Pfam and InterPro IPR001890

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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CRS1 / YhbY (CRM) domain Provide feedback

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants [4]. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing [5]. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes [4]. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [1].

Literature references

  1. Ostheimer GJ, Barkan A, Matthews BW; , Structure (Camb) 2002;10:1593-1601.: Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins. PUBMED:12429100 EPMC:12429100

  2. Willis MA, Krajewski W, Chalamasetty VR, Reddy P, Howard A, Herzberg O; , Proteins 2002;49:423-426.: Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus influenzae. PUBMED:12360533 EPMC:12360533

  3. Till B, Schmitz-Linneweber C, Williams-Carrier R, Barkan A; , RNA 2001;7:1227-1238.: CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. PUBMED:11565746 EPMC:11565746

  4. Barkan A, Klipcan L, Ostersetzer O, Kawamura T, Asakura Y, Watkins KP; , RNA. 2007;13:55-64.: The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. PUBMED:17105995 EPMC:17105995

  5. Asakura Y, Barkan A; , Plant Cell. 2007;19:3864-3875.: A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts. PUBMED:18065687 EPMC:18065687


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001890

The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (SWISSPROT), CAF1 (SWISSPROT) and CAF2 (SWISSPROT) proteins and the Escherichia coli protein YhbY (SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [PUBMED:12881426, PUBMED:17105995].

The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue [PUBMED:12429100].

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants [PUBMED:17105995]. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing [PUBMED:18065687]. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes [PUBMED:17105995]. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [PUBMED:11565746].

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  Seed
(144)
Full
(3330)
Representative proteomes NCBI
(1854)
Meta
(228)
RP15
(200)
RP35
(497)
RP55
(697)
RP75
(855)
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  Seed
(144)
Full
(3330)
Representative proteomes NCBI
(1854)
Meta
(228)
RP15
(200)
RP35
(497)
RP55
(697)
RP75
(855)
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Seed source: Enright A
Previous IDs: UPF0044;
Type: Domain
Author: Enright A, Ouzounis C, Bateman A
Number in seed: 144
Number in full: 3330
Average length of the domain: 83.80 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 62.62 %

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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 20.8 20.8
Trusted cut-off 21.1 21.4
Noise cut-off 19.6 19.8
Model length: 84
Family (HMM) version: 16
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Interactions

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CRS1_YhbY

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 CRS1_YhbY domain has been found. There are 4 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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