Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
163  structures 3393  species 2  interactions 3444  sequences 9  architectures

Family: YgbB (PF02542)

Summary: YgbB family

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 "YgbB N terminal protein domain". More...

YgbB N terminal protein domain Edit Wikipedia article

YgbB
PDB 1vh8 EBI.jpg
crystal structure of a 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase
Identifiers
Symbol YgbB
Pfam PF02542
InterPro IPR003526
SCOP 1iv1
SUPERFAMILY 1iv1
CDD cd0554

In molecular biology, YgbB is a protein domain. This entry makes reference to a number of proteins from eukaryotes and prokaryotes which share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme thought to aid terpenoid and isoprenoid biosynthesis, a vital chemical in all living organisms. This protein domain is part of an enzyme which catalyses a reaction in a complex pathway. [1]

Function

The YgbB protein domain has a main function of being involved in terpenoid and isoprenoid biosynthesis.

Biochemistry

MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis.[2]

  1. ^ Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F (March 2000). "Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate". Proc. Natl. Acad. Sci. U.S.A. 97 (6): 2486–90. doi:10.1073/pnas.040554697. PMC 15955. PMID 10694574. 
  2. ^ Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY (January 2003). "Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis". Acta Crystallogr. D Biol. Crystallogr. 59 (Pt 1): 23–31. doi:10.1107/s0907444902017705. PMID 12499535. 

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.

YgbB family Provide feedback

The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis) [1].

Literature references

  1. Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F; , Proc Natl Acad Sci U S A 2000;97:2486-2490.: Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate. PUBMED:10694574 EPMC:10694574


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003526

IspF is a MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, also known as YgbB. It is an enzyme in the non-mevalonate pathway of isoprenoid synthesis. Isoprenoids are essential in all organisms, and can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[PUBMED:12499535].

A number of proteins from eukaryotes and prokaryotes are bifunctional proteins with an N-terminal IspD domain and a C-terminal IspF domain [PUBMED:15233799].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

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
(167)
Full
(3444)
Representative proteomes NCBI
(2387)
Meta
(2171)
RP15
(298)
RP35
(571)
RP55
(724)
RP75
(843)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(167)
Full
(3444)
Representative proteomes NCBI
(2387)
Meta
(2171)
RP15
(298)
RP35
(571)
RP55
(724)
RP75
(843)
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
(167)
Full
(3444)
Representative proteomes NCBI
(2387)
Meta
(2171)
RP15
(298)
RP35
(571)
RP55
(724)
RP75
(843)
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.

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: COGs
Previous IDs: none
Type: Family
Author: Mian N, Bateman A
Number in seed: 167
Number in full: 3444
Average length of the domain: 155.90 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 76.19 %

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 25.0 25.0
Trusted cut-off 26.2 26.4
Noise cut-off 24.8 22.7
Model length: 157
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

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

YgbB IspD

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 YgbB domain has been found. There are 163 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.

Loading structure mapping...