PPDK pyruvate orthophosphate dikinase [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: PPDK
Official Full Name: pyruvate orthophosphate dikinase
Primary source: TAIR:AT4G15530
Locus tag: AT4G15530
See related: Araport:AT4G15530
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: DL3805C; FCAALL.325; pyruvate orthophosphate dikinase
Summary: Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues.
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Genomic context

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See PPDK in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 19

Sequence:: Chromosome: 4; NC_003075.7 (8864615..8870979, complement)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment, one is via PCK1, and a second via PPDK.
Title: Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment.
Over-expression of PPDK during senescence increases nitrogen remobilization from senescing leaves and increases seed size and seed nitrogen content.
Title: Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content.
In cotyledons pyruvate orthophosphate dikinase may be important in supplying phosphoenol pyruvate to gluconeogenesis, and in ageing leaves it allows remobilisation of nitrogen to supply reproductive tissue [pyruvate orthophosphate dikinase] [PPDK]
Title: The Arabidopsis PPDK gene is transcribed from two promoters to produce differentially expressed transcripts responsible for cytosolic and plastidic proteins.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001036570.1

Supported by ESTs:

NM_001084926.1

Supported by ESTs:

NM_001084927.2

Supported by ESTs:

NM_001125515.1

Supported by ESTs:

NM_001341051.1

Supported by ESTs:

NM_117643.4

Supported by ESTs:

NM_179060.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables pyruvate, phosphate dikinase activity	IEA Inferred from Electronic Annotation more info
enables pyruvate, phosphate dikinase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
involved_in pyruvate metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chloroplast	HDA more info	PubMed
located_in chloroplast	IDA Inferred from Direct Assay more info	PubMed
located_in chloroplast	ISM Inferred from Sequence Model more info
located_in chloroplast stroma	HDA more info	PubMed
located_in cytosol	HDA more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
NOT located_in cytosol	RCA inferred from Reviewed Computational Analysis more info	PubMed

General protein information

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Preferred Names: pyruvate orthophosphate dikinase

NP_001031647.1

pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).

NP_001078395.1

pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15226 Blast hits to 15137 proteins in 2575 species: Archae - 291; Bacteria - 9909; Metazoa - 12; Fungi - 19; Plants - 160; Viruses - 0; Other Eukaryotes - 4835 (source: NCBI BLink).

NP_001078396.1

pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), Pyruvate, phosphate dikinase (InterPro:IPR010121), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15119 Blast hits to 15038 proteins in 2560 species: Archae - 291; Bacteria - 9841; Metazoa - 12; Fungi - 19; Plants - 125; Viruses - 0; Other Eukaryotes - 4831 (source: NCBI BLink).

NP_001118987.1

pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile domain (InterPro:IPR008279), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NP_193288.2

pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15214 Blast hits to 15125 proteins in 2575 species: Archae - 291; Bacteria - 9898; Metazoa - 12; Fungi - 19; Plants - 160; Viruses - 0; Other Eukaryotes - 4834 (source: NCBI BLink).

NP_849391.2

pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast stroma, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15301 Blast hits to 15212 proteins in 2599 species: Archae - 294; Bacteria - 9981; Metazoa - 12; Fungi - 19; Plants - 160; Viruses - 0; Other Eukaryotes - 4835 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003075.7 Reference assembly

Range

8864615..8870979 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_117643.4 → NP_193288.2 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_193288.2

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UZQ3, B9DHM5

Conserved Domains (4) summary

PRK09279
Location:1 → 871

PRK09279; pyruvate phosphate dikinase; Provisional

pfam00391
Location:426 → 505

PEP-utilizers; PEP-utilizing enzyme, mobile domain

pfam01326
Location:23 → 359

PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain

pfam02896
Location:517 → 872

PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain
NM_179060.4 → NP_849391.2 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_849391.2

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9XSP5, A0A654FPJ2

Conserved Domains (1) summary

PRK09279
Location:84 → 952

PRK09279; pyruvate phosphate dikinase; Provisional
NM_001084926.1 → NP_001078395.1 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001078395.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9XSP5, A0A654FPJ2

Conserved Domains (1) summary

PRK09279
Location:84 → 952

PRK09279; pyruvate phosphate dikinase; Provisional
NM_001036570.1 → NP_001031647.1 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001031647.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UZQ3

Conserved Domains (4) summary

PRK09279
Location:1 → 853

PRK09279; pyruvate phosphate dikinase; Provisional

pfam00391
Location:408 → 487

PEP-utilizers; PEP-utilizing enzyme, mobile domain

pfam01326
Location:5 → 341

PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain

pfam02896
Location:499 → 854

PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain
NM_001084927.2 → NP_001078396.1 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001078396.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DGK5, O23404, Q27GJ5, Q2V3I1, Q3EA16

UniProtKB/TrEMBL

A0A5S9XSP5

Conserved Domains (4) summary

PRK09279
Location:91 → 959

PRK09279; pyruvate phosphate dikinase; Provisional

pfam00391
Location:514 → 593

PEP-utilizers; PEP-utilizing enzyme, mobile domain

pfam01326
Location:111 → 447

PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain

pfam02896
Location:605 → 960

PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain
NM_001125515.1 → NP_001118987.1 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001118987.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DGK5, O23404, Q27GJ5, Q2V3I1, Q3EA16

UniProtKB/TrEMBL

A0A5S9XSP5

Conserved Domains (4) summary

PRK09279
Location:91 → 959

PRK09279; pyruvate phosphate dikinase; Provisional

pfam00391
Location:514 → 593

PEP-utilizers; PEP-utilizing enzyme, mobile domain

pfam01326
Location:111 → 447

PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain

pfam02896
Location:605 → 960

PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain
NM_001341051.1 → NP_001328869.1 pyruvate orthophosphate dikinase [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UZQ3