Q4FM31 (ISPDF_PELUB) Reviewed, UniProtKB/Swiss-Prot
Last modified
January 25, 2012.
Version 45.
History...
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Bifunctional enzyme IspD/IspF Including the following 2 domains: | ||||
| Gene names |
| ||||
| Organism | Pelagibacter ubique (strain HTCC1062) [Complete proteome] [HAMAP] | ||||
| Taxonomic identifier | 335992 [NCBI] | ||||
| Taxonomic lineage | Bacteria › Proteobacteria › Alphaproteobacteria › Rickettsiales › SAR11 cluster › Candidatus Pelagibacter |
Protein attributes
| Sequence length | 371 AA. |
| Sequence status | Complete. |
| Protein existence | Inferred from homology |
General annotation (Comments)
| Function | Bifunctional enzyme that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP) (IspD), and converts 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) and CMP (IspF) By similarity. HAMAP MF_01520 |
| Catalytic activity | CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. HAMAP MF_01520 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP. HAMAP MF_01520 |
| Cofactor | Divalent metal cations By similarity. HAMAP MF_01520 |
| Pathway | Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. HAMAP MF_01520 |
| Sequence similarities | In the N-terminal section; belongs to the IspD family. In the C-terminal section; belongs to the IspF family. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Isoprene biosynthesis |
| Ligand | Metal-binding |
| Molecular function | Lyase Nucleotidyltransferase Transferase |
| Technical term | Complete proteome Multifunctional enzyme |
| Gene Ontology (GO) | |
| Biological process | terpenoid biosynthetic process Inferred from electronic annotation. Source: InterPro |
| Molecular function | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Inferred from electronic annotation. Source: EC 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activityInferred from electronic annotation. Source: EC metal ion bindingInferred from electronic annotation. Source: UniProtKB-KW |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 371 | 371 | Bifunctional enzyme IspD/IspF HAMAP MF_01520 | PRO_0000075672 | |||||
Regions | |||||||||
| Region | 1 – 214 | 214 | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520 | ||||||
| Region | 215 – 371 | 157 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP MF_01520 | ||||||
Sites | |||||||||
| Metal binding | 221 | 1 | Divalent metal cation By similarity | ||||||
| Metal binding | 223 | 1 | Divalent metal cation By similarity | ||||||
| Metal binding | 255 | 1 | Divalent metal cation By similarity | ||||||
| Site | 15 | 1 | Transition state stabilizer By similarity | ||||||
| Site | 22 | 1 | Transition state stabilizer By similarity | ||||||
| Site | 148 | 1 | Positions MEP for the nucleophilic attack By similarity | ||||||
| Site | 201 | 1 | Positions MEP for the nucleophilic attack By similarity | ||||||
| Site | 247 | 1 | Transition state stabilizer By similarity | ||||||
| Site | 346 | 1 | Transition state stabilizer By similarity | ||||||
Sequences
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References
| [1] | "Genome streamlining in a cosmopolitan oceanic bacterium." Giovannoni S.J., Tripp H.J., Givan S., Podar M., Vergin K.L., Baptista D., Bibbs L., Eads J., Richardson T.H., Noordewier M., Rappe M.S., Short J.M., Carrington J.C., Mathur E.J. Science 309:1242-1245(2005) [PubMed: 16109880] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: HTCC1062. |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | CP000084 Genomic DNA. Translation: AAZ21757.1. |
| RefSeq | YP_266361.1. NC_007205.1. |
3D structure databases | |
| ProteinModelPortal | Q4FM31. |
| ModBase | Search... |
Protocols and materials databases | |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| GeneID | 3516956. |
| GenomeReviews | Gene locus SAR11_0945 in contig CP000084_GR. |
| KEGG | pub:SAR11_0945. |
| PATRIC | 31991373. VBICanPel5618_0940. |
Organism-specific databases | |
| CMR | Search... |
Phylogenomic databases | |
| eggNOG | COG1211. |
| HOGENOM | HBG672839. |
| OMA | IVLIHDA. |
| PhylomeDB | Q4FM31. |
Enzyme and pathway databases | |
| BioCyc | CPEL335992:SAR11_0945-MONOMER. |
Family and domain databases | |
| HAMAP | MF_01520. IspDF. [Tree] |
| InterPro | IPR023423. IpsF_dom. IPR001228. ISPD_synthase. IPR018294. ISPD_synthase_CS. IPR003526. MECDP_synthase. IPR020555. MECDP_synthase_CS. [Graphical view] |
| Gene3D | G3DSA:3.30.1330.50. MECDP_synthase_core. 1 hit. |
| KO | K12506. |
| Pfam | PF01128. IspD. 1 hit. PF02542. YgbB. 1 hit. [Graphical view] |
| SUPFAM | SSF69765. YgbB_synth. 1 hit. |
| TIGRFAMs | TIGR00453. IspD. 1 hit. TIGR00151. IspF. 1 hit. |
| PROSITE | PS01295. ISPD. 1 hit. PS01350. ISPF. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Entry information
| Entry name | ISPDF_PELUB | ||||||||
| Accession | Primary (citable) accession number: Q4FM31 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Prokaryotic Protein Annotation Program | ||||||||
Relevant documents
| PATHWAY comments Index of metabolic and biosynthesis pathways |
| SIMILARITY comments Index of protein domains and families |

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