Summary: YgbB family
This is the Wikipedia entry entitled "YgbB N terminal protein domain". More...
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YgbB N terminal protein domain Edit Wikipedia article
crystal structure of a 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase
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. 
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.
- 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.
- 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.
YgbB family Provide feedback
The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis) .
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity (GO:0008685)|
|Biological process||terpenoid biosynthetic process (GO:0016114)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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Curation and family details
|Author:||Mian N, Bateman A|
|Number in seed:||751|
|Number in full:||1407|
|Average length of the domain:||154.10 aa|
|Average identity of full alignment:||46 %|
|Average coverage of the sequence by the domain:||74.36 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 177 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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