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13  structures 8545  species 0  interactions 10545  sequences 59  architectures

Family: YchF-GTPase_C (PF06071)

Summary: Protein of unknown function (DUF933)

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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
SymbolYchF-GTPase_C
PfamPF06071
Pfam clanCL0072
InterProIPR013029
SCOP21ni3 / SCOPe / SUPFAM
CDDcd04867

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

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

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

  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. doi:10.1046/j.1365-2958.2001.02536.x. 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. doi:10.1128/jb.185.14.4031-4037.2003. PMC 164861. PMID 12837776.
This article incorporates text from the public domain Pfam and InterPro: IPR013029

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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 YchF. The crystal structure of YchF 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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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...

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
(353)
Full
(10545)
Representative proteomes UniProt
(45014)
RP15
(1682)
RP35
(5258)
RP55
(10312)
RP75
(16891)
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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
(353)
Full
(10545)
Representative proteomes UniProt
(45014)
RP15
(1682)
RP35
(5258)
RP55
(10312)
RP75
(16891)
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
(353)
Full
(10545)
Representative proteomes UniProt
(45014)
RP15
(1682)
RP35
(5258)
RP55
(10312)
RP75
(16891)
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: Pfam-B_10000 (release 9.0)
Previous IDs: DUF933;
Type: Domain
Sequence Ontology: SO:0000417
Author: Moxon SJ , Studholme DJ
Number in seed: 353
Number in full: 10545
Average length of the domain: 83.50 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 22.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.3 29.4
Noise cut-off 26.7 26.6
Model length: 84
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 YchF-GTPase_C domain has been found. There are 13 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
A0A0R4J410 View 3D Structure Click here
A0A1D6FIL5 View 3D Structure Click here
A0A1D6HK39 View 3D Structure Click here
A0A1D6IYG6 View 3D Structure Click here
A0A1D6LFA3 View 3D Structure Click here
A0A1D8PDE8 View 3D Structure Click here
A0A1D8PQE7 View 3D Structure Click here
A0JPJ7 View 3D Structure Click here
A4I2Y9 View 3D Structure Click here
A4I330 View 3D Structure Click here
B8BBN7 View 3D Structure Click here
C0PGN4 View 3D Structure Click here
F4I3J0 View 3D Structure Click here
K7L8F3 View 3D Structure Click here
O13998 View 3D Structure Click here
O14078 View 3D Structure Click here
O53459 View 3D Structure Click here
P0ABU2 View 3D Structure Click here
P0ABU3 View 3D Structure Click here
P0ABU4 View 3D Structure Click here
P37518 View 3D Structure Click here
P38219 View 3D Structure Click here
P38746 View 3D Structure Click here
P44681 View 3D Structure Click here
P47270 View 3D Structure Click here
P57288 View 3D Structure Click here
P75088 View 3D Structure Click here
P91917 View 3D Structure Click here
Q2G115 View 3D Structure Click here
Q2HJ33 View 3D Structure Click here
Q4CN17 View 3D Structure Click here
Q4DGJ5 View 3D Structure Click here
Q4DNY5 View 3D Structure Click here
Q4DTU3 View 3D Structure Click here
Q54CY8 View 3D Structure Click here
Q55ET7 View 3D Structure Click here
Q5R821 View 3D Structure Click here
Q5ZM25 View 3D Structure Click here
Q66JG0 View 3D Structure Click here
Q6Z1J6 View 3D Structure Click here