Q59754 · PPDK_RHIME
- ProteinPyruvate, phosphate dikinase
- GeneppdK
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids898 (go to sequence)
- Protein existenceInferred from homology
- Annotation score4/5
Function
function
Catalyzes the reversible phosphorylation of pyruvate and phosphate.
Miscellaneous
The reaction takes place in three steps, each mediated by a carrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain.
Catalytic activity
- pyruvate + phosphate + ATP = phosphoenolpyruvate + AMP + diphosphate + H+
Cofactor
Activity regulation
Activated by light-induced dephosphorylation. Inhibited by dark-induced phosphorylation. Both reactions are catalyzed by PDRP1 (By similarity).
Features
Showing features for binding site, active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 96 | ATP (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Active site | 468 | Tele-phosphohistidine intermediate | ||||
Sequence: H | ||||||
Binding site | 574 | substrate | ||||
Sequence: R | ||||||
Binding site | 630 | substrate | ||||
Sequence: R | ||||||
Binding site | 758 | Mg2+ (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 758 | substrate | ||||
Sequence: E | ||||||
Binding site | 779 | substrate | ||||
Sequence: G | ||||||
Binding site | 780 | substrate | ||||
Sequence: T | ||||||
Binding site | 781 | substrate | ||||
Sequence: N | ||||||
Binding site | 782 | Mg2+ (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 782 | substrate | ||||
Sequence: D | ||||||
Active site | 844 | Proton donor | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Molecular Function | ATP binding | |
Molecular Function | kinase activity | |
Molecular Function | metal ion binding | |
Molecular Function | pyruvate, phosphate dikinase activity | |
Biological Process | phosphorylation | |
Biological Process | pyruvate metabolic process |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended namePyruvate, phosphate dikinase
- EC number
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Alphaproteobacteria > Hyphomicrobiales > Rhizobiaceae > Sinorhizobium/Ensifer group > Sinorhizobium
Accessions
- Primary accessionQ59754
- Secondary accessions
Proteomes
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000147047 | 1-898 | Pyruvate, phosphate dikinase | |||
Sequence: MAKWVYTFGAGQAEGSAEDRDRLGGKGANLAEMCNLGLPVPPGLTIVTAACNSYLEKGRSMPEGLREQVREGITRMEKITGRVFGDTNRPLLLSVRSGARASMPGMMDTVLNLGLNDQSVHALGHDAGDARFAWDSYRRFIQMYGDVVMGVDHEVFEEVLEDEKARLGHEQDTELSAVEWQHVISRYKEAIEEVLGLPFPQDPEVQLWGAIGAVFSSWMNPRAITYRHLHGIPAGWGTAVNVQAMVFGNLGNSSATGVAFTRNPSTGEKELYGEFLVNAQGEDVVAGIRTPQNITEAARIASGSDKPSLEKLMPEAFAEFEKICNALERHYRDMQDIEFTIERGKLWMLQTRSGKRTAKSALKIAVDMAEEGLISKEEAVARIDPASLDQLLHPTIDPHARRDIIGSGLPASPGAATGEIVFSSDEAVQAVKEGRKVILVRVETSPEDIHGMHAAEGILTTRGGMTSHAAVVARGMGTPCVSGAGSIRVDQRNELLIAASVTLRKGDVITIDGSSGQVLKGEIPMLQPELSGDFGKIMQWADASRRMTVRTNAETPADARAARSFGAEGIGLCRTEHMFFEDDRINVMREMILAEDEAGRRTALAKLLPMQRSDFVELFSIMHGLPVTIRLLDPPLHEFLPKTDEEIAEVARVLTIDPAELRQRVDALHEFNPMLGHRGCRLAISYPEIAEMQARAIFEAAVQAAHDTGAAVVPEIMVPLVGLRAELDYVKARIEAVAKEVIGEAGVNIDYLIGTMIELPRAALRADTIAESADFFSFGTNDLTQTTFGISRDDAALFLATYQQKGIIEQDPFVSLDFEGVGELIQIAAERGRRTKNGLKLGICGEHGGDPASIRFCEEAGLDYVSCSPFRVPIARLAAAQATINGREVAEVQALAAS | ||||||
Modified residue | 466 | Phosphothreonine; by PDRP1 | ||||
Sequence: T |
Post-translational modification
Phosphorylation of Thr-466 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme (By similarity).
Keywords
- PTM
Interaction
Subunit
Homodimer.
Structure
Family & Domains
Features
Showing features for region.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-355 | N-terminal | ||||
Sequence: MAKWVYTFGAGQAEGSAEDRDRLGGKGANLAEMCNLGLPVPPGLTIVTAACNSYLEKGRSMPEGLREQVREGITRMEKITGRVFGDTNRPLLLSVRSGARASMPGMMDTVLNLGLNDQSVHALGHDAGDARFAWDSYRRFIQMYGDVVMGVDHEVFEEVLEDEKARLGHEQDTELSAVEWQHVISRYKEAIEEVLGLPFPQDPEVQLWGAIGAVFSSWMNPRAITYRHLHGIPAGWGTAVNVQAMVFGNLGNSSATGVAFTRNPSTGEKELYGEFLVNAQGEDVVAGIRTPQNITEAARIASGSDKPSLEKLMPEAFAEFEKICNALERHYRDMQDIEFTIERGKLWMLQTRSGK | ||||||
Region | 356-412 | Linker 1 | ||||
Sequence: RTAKSALKIAVDMAEEGLISKEEAVARIDPASLDQLLHPTIDPHARRDIIGSGLPAS | ||||||
Region | 413-511 | Central | ||||
Sequence: PGAATGEIVFSSDEAVQAVKEGRKVILVRVETSPEDIHGMHAAEGILTTRGGMTSHAAVVARGMGTPCVSGAGSIRVDQRNELLIAASVTLRKGDVITI | ||||||
Region | 512-546 | Linker 2 | ||||
Sequence: DGSSGQVLKGEIPMLQPELSGDFGKIMQWADASRR | ||||||
Region | 547-898 | C-terminal | ||||
Sequence: MTVRTNAETPADARAARSFGAEGIGLCRTEHMFFEDDRINVMREMILAEDEAGRRTALAKLLPMQRSDFVELFSIMHGLPVTIRLLDPPLHEFLPKTDEEIAEVARVLTIDPAELRQRVDALHEFNPMLGHRGCRLAISYPEIAEMQARAIFEAAVQAAHDTGAAVVPEIMVPLVGLRAELDYVKARIEAVAKEVIGEAGVNIDYLIGTMIELPRAALRADTIAESADFFSFGTNDLTQTTFGISRDDAALFLATYQQKGIIEQDPFVSLDFEGVGELIQIAAERGRRTKNGLKLGICGEHGGDPASIRFCEEAGLDYVSCSPFRVPIARLAAAQATINGREVAEVQALAAS |
Domain
The N-terminal domain contains the ATP/Pi active site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate active site.
Sequence similarities
Belongs to the PEP-utilizing enzyme family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length898
- Mass (Da)97,561
- Last updated2000-05-30 v2
- ChecksumD055560636388CD5
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 88 | in Ref. 3; AAB58818 | ||||
Sequence: N → I | ||||||
Sequence conflict | 128 | in Ref. 3; AAB58818 | ||||
Sequence: G → D | ||||||
Sequence conflict | 711-712 | in Ref. 3 | ||||
Sequence: AV → LL | ||||||
Sequence conflict | 722-723 | in Ref. 3 | ||||
Sequence: GL → V | ||||||
Sequence conflict | 736-738 | in Ref. 3; AAB58820 | ||||
Sequence: AVA → DGR |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AL591688 EMBL· GenBank· DDBJ | CAC45504.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AH005244 EMBL· GenBank· DDBJ | AAB58818.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AH005244 EMBL· GenBank· DDBJ | AAB58819.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AH005244 EMBL· GenBank· DDBJ | AAB58820.1 EMBL· GenBank· DDBJ | Genomic DNA |