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7  structures 4777  species 2  interactions 5012  sequences 16  architectures

Family: YchF-GTPase_C (PF06071)

Summary: Protein of unknown function (DUF933)

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 "YchF-GTPase C terminal protein domain". More...

YchF-GTPase C terminal protein domain Edit Wikipedia article

C terminal domain of YchF-GTPase
PDB 1jal EBI.jpg
ychf protein (hi0393)
Identifiers
Symbol YchF-GTPase_C
Pfam PF06071
Pfam clan CL0072
InterPro IPR013029
SCOP 1ni3
SUPERFAMILY 1ni3
CDD cd04867

In molecular biology, this protein domain is found at the C terminus of the GTP-binding protein, YchF-GTPase found in both prokaryotes and eukaryotes.

Function[edit]

The function of this protein domain remains unknown, however, it is putatively thought to be necessary for ribosome function or for signal transduction from the ribosome to downstream targets. Additionally, GTPases are often described as a molecular switch. [1]

Structure[edit]

The crystal structure of Haemophilus influenzae has been determined.[2] This protein consists of three domains, of which the C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix.

References[edit]

  1. ^ Caldon CE, Yoong P, March PE (2001). "Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function.". Mol Microbiol 41 (2): 289–97. PMID 11489118. 
  2. ^ Teplyakov A, Obmolova G, Chu SY, Toedt J, Eisenstein E, Howard AJ, Gilliland GL (July 2003). "Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid". J. Bacteriol. 185 (14): 4031–7. PMC 164861. PMID 12837776. 

This article incorporates text from the public domain Pfam and InterPro IPR013029

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.

Protein of unknown function (DUF933) Provide feedback

This domain is found at the C terminus of the YchF GTP-binding protein (O13998) and is possibly related to the ubiquitin-like and MoaD/ThiS superfamilies.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013029

This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of SWISSPROT from Haemophilus influenzae has been determined [PUBMED:12837776]. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Ubiquitin (CL0072), which has the following description:

This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.

The clan contains the following 41 members:

APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF1315 DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD

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...

View options

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
(44)
Full
(5012)
Representative proteomes NCBI
(3379)
Meta
(2253)
RP15
(463)
RP35
(849)
RP55
(1106)
RP75
(1296)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(44)
Full
(5012)
Representative proteomes NCBI
(3379)
Meta
(2253)
RP15
(463)
RP35
(849)
RP55
(1106)
RP75
(1296)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(44)
Full
(5012)
Representative proteomes NCBI
(3379)
Meta
(2253)
RP15
(463)
RP35
(849)
RP55
(1106)
RP75
(1296)
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: Pfam-B_10000 (release 9.0)
Previous IDs: DUF933;
Type: Domain
Author: Moxon SJ, Studholme DJ
Number in seed: 44
Number in full: 5012
Average length of the domain: 82.60 aa
Average identity of full alignment: 63 %
Average coverage of the sequence by the domain: 22.65 %

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 20.1 20.1
Trusted cut-off 20.7 20.5
Noise cut-off 19.7 19.9
Model length: 84
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 2 interactions for this family. More...

MMR_HSR1 YchF-GTPase_C

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 YchF-GTPase_C 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 seqence.

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