Pseudomonas aeruginosa PAO1, PA3627 (ygbB)

Cytoplasmic
Cytoplasmic Membrane
Periplasmic
Outer Membrane
Extracellular
Unknown
View in JBrowse PseudoCyc / Metabolic Pathways

Gene Feature Overview

Strain Pseudomonas aeruginosa PAO1 (Stover et al., 2000)
GCF_000006765.1|latest
Locus Tag
PA3627
Name
ygbB
Replicon chromosome
Genomic location 4062426 - 4062899 (- strand)
Transposon Mutants 1 transposon mutants in PAO1

Cross-References

RefSeq NP_252317.1
GI 15598823
Affymetrix PA3627_at
DNASU PaCD00007589
Entrez 880484
GenBank AAG07015.1
INSDC AAG07015.1
NCBI Locus Tag PA3627
protein_id(GenBank) gb|AAG07015.1|AE004782_13|gnl|PseudoCAP|PA3627
TIGR NTL03PA03627
UniParc UPI000012D976
UniProtKB Acc P57708
UniProtKB ID ISPF_PSEAE
UniRef100 UniRef100_B7V8C1
UniRef50 UniRef50_Q5L8X2
UniRef90 UniRef90_A6V1G1

Product

Feature Type CDS
Coding Frame 1
Product Name
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Product Name Confidence: Class 2
Synonyms YgbB protein
Evidence for Translation
Identified using nanoflow high-pressure liquid chromatography (HPLC) in conjunction with microelectrospray ionization on LTQ XL mass spectrometer (PMID:24291602).
Charge (pH 7) 0.39
Kyte-Doolittle Hydrophobicity Value 0.086
Molecular Weight (kDa) 16.7
Isoelectric Point (pI) 7.10

Subcellular localization

Individual Mappings
Localization Confidence PMID
Cytoplasmic Class 3
Additional evidence for subcellular localization

AlphaFold 2 Protein Structure Predictions

Protein structure predictions using a neural network model developed by DeepMind. If a UniProtKB accession is associated with this protein, a search link will be provided below.

Look for predicted 3D structure in AlphaFold DB: Search

PDB 3D Structures

Accession Header Accession Date Compound Source Resolution Method Percent Identity
5B8F LYASE 04/20/15 X-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Pseudomonas aeruginosa Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) 1.45 X-RAY DIFFRACTION 100.0

Pathogen Association Analysis

Results
Common
Found in both pathogen and nonpathogenic strains
Hits to this gene were found in 520 genera

Orthologs/Comparative Genomics

Pseudomonas Ortholog Database View orthologs at Pseudomonas Ortholog Database
Pseudomonas Ortholog Group POG002047 (537 members)
Putative Inparalogs None Found

Interactions

STRING database Search for predicted protein-protein interactions using:
Search term: PA3627
Search term: ygbB

Human Homologs

References

Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate.
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 Mar 14;97(6):2486-90
PubMed ID: 10694574