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P11155 (PPDK1_MAIZE) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 101. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pyruvate, phosphate dikinase 1, chloroplastic
EC=2.7.9.1
Alternative name(s):
Pyruvate, orthophosphate dikinase 1
Gene names
Name:PPDK1
Synonyms:C4PPDKZM1, CYPPDKZM1
OrganismZea mays (Maize)
Taxonomic identifier4577 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › PACMAD clade › Panicoideae › Andropogoneae › Zea

Protein attributes

Sequence length947 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Formation of phosphoenolpyruvate, which is the primary acceptor of CO2 in C4 and some Crassulacean acid metabolism plants. Ref.5

Catalytic activity

ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate.

Cofactor

Magnesium.

Enzyme regulation

Activated by light-induced dephosphorylation. Inhibited by dark-induced phosphorylation. Both reactions are catalyzed by PDRP1. Inactivated by cold due to the dissociation of the homotetramer. Ref.7 Ref.8 Ref.10

Pathway

Photosynthesis; C4 acid pathway.

Subunit structure

Homotetramer.

Subcellular location

Plastid › chloroplast. Cytoplasm. Note: Isoform 1 is targeted to the chloroplast while isoform 2 is found in the cytoplasm. Ref.5

Tissue specificity

Isoform 1 mainly localized in mesophyll cells and only a low level is found in bundle sheath cells. Isoform 2 expressed in roots, stems and etiolated leaves. Ref.3 Ref.5

Induction

Isoform 1 is light-inducible. Ref.5 Ref.7 Ref.8 Ref.10

Domain

The N-terminal domain contains the ATP/Pi binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate binding site.

Post-translational modification

Phosphorylation of Thr-527 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme.

Miscellaneous

The reaction takes place in three steps, mediated by a phosphocarrier 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.

Ref.5 shows the existence of a second gene coding only for the short cytoplasmic isoform of PPDK.

Sequence similarities

Belongs to the PEP-utilizing enzyme family.

Biophysicochemical properties

Kinetic parameters:

KM=158 µM for pyruvate Ref.8

KM=95 µM for ATP

KM=408 µM for phosphate

Temperature dependence:

Loss of activity below 10 degrees Celsius.

Sequence caution

The sequence AAA33495.1 differs from that shown. Reason: Frameshift at positions 43 and 56.

Alternative products

This entry describes 2 isoforms produced by alternative promoter usage. [Align] [Select]
Isoform 1 (identifier: P11155-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P11155-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-64: Missing.
     65-75: VDAAPIQTTKK → MAPAPCGRSSQ
Note: Produced by alternative promoter usage. Cytoplasmic.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier
Sequence conflict4 – 96APCGRS → VQCAR in AAB23731. Ref.5

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 7171Chloroplast
Chain72 – 947876Pyruvate, phosphate dikinase 1, chloroplastic
PRO_0000023563

Sites

Active site5291Tele-phosphohistidine intermediate Ref.10
Active site9071Proton donor Probable
Metal binding8211Magnesium
Metal binding8451Magnesium
Binding site6351Substrate
Binding site6921Substrate
Binding site8211Substrate By similarity
Binding site8421Substrate; via carbonyl oxygen By similarity
Binding site8431Substrate; via amide nitrogen By similarity
Binding site8441Substrate
Binding site8451Substrate; via amide nitrogen

Amino acid modifications

Modified residue5271Phosphothreonine; by PDRP1 Ref.4

Natural variations

Alternative sequence1 – 6464Missing in isoform 2.
VSP_034609
Alternative sequence65 – 7511VDAAPIQTTKK → MAPAPCGRSSQ in isoform 2.
VSP_034610

Experimental info

Mutagenesis5271T → D or E: Abolished activity. Ref.9 Ref.10
Mutagenesis5271T → N: Greatly reduced activity. Ref.9 Ref.10
Mutagenesis5271T → S or V: No effect on activity. Ref.9 Ref.10
Mutagenesis5271T → Y: Greatly reduced activity. No tyrosine phosphorylation by PDRP1 in vitro. Ref.9 Ref.10
Mutagenesis5291H → N: Abolished activity. No phosphorylation on T-527 by PDRP1 in vitro. Ref.10
Mutagenesis9461L → V: No decrease of the cold sensitivity. Ref.8
Sequence conflict21A → T in AAA33498. Ref.2
Sequence conflict21A → T in AAB23730. Ref.5
Sequence conflict5361W → G in AAA33498. Ref.2
Sequence conflict5611S → G in AAA33498. Ref.2
Sequence conflict6711T → P in AAA33498. Ref.2
Sequence conflict696 – 6994HPSY → PPLH in AAA33498. Ref.2
Sequence conflict8651H → Y in AAA33498. Ref.2
Sequence conflict869 – 8735GILQH → EFGTS in AAD45281. Ref.6
Sequence conflict8901F → L in AAA33498. Ref.2
Sequence conflict9271F → Y in AAA33498. Ref.2
Sequence conflict9271F → Y in AAD45281. Ref.6

Secondary structure

1 ....................................................................................................................................................... 947
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 1, 2008. Version 2.
Checksum: 6D11F51D150ACFD1

FASTA947102,674
        10         20         30         40         50         60 
MAASVSRAIC VQKPGSKCTR DREATSFARR SVAAPRPPHA KAAGVIRSDS GAGRGQHCSP 

        70         80         90        100        110        120 
LRAVVDAAPI QTTKKRVFHF GKGKSEGNKT MKELLGGKGA NLAEMASIGL SVPPGFTVST 

       130        140        150        160        170        180 
EACQQYQDAG CALPAGLWAE IVDGLQWVEE YMGATLGDPQ RPLLLSVRSG AAVSMPGMMD 

       190        200        210        220        230        240 
TVLNLGLNDE VAAGLAAKSG ERFAYDSFRR FLDMFGNVVM DIPRSLFEEK LEHMKESKGL 

       250        260        270        280        290        300 
KNDTDLTASD LKELVGQYKE VYLSAKGEPF PSDPKKQLEL AVLAVFNSWE SPRAKKYRSI 

       310        320        330        340        350        360 
NQITGLRGTA VNVQCMVFGN MGNTSGTGVL FTRNPNTGEK KLYGEFLVNA QGEDVVAGIR 

       370        380        390        400        410        420 
TPEDLDAMKN LMPQAYDELV ENCNILESHY KEMQDIEFTV QENRLWMLQC RTGKRTGKSA 

       430        440        450        460        470        480 
VKIAVDMVNE GLVEPRSAIK MVEPGHLDQL LHPQFENPSA YKDQVIATGL PASPGAAVGQ 

       490        500        510        520        530        540 
VVFTAEDAEA WHSQGKAAIL VRAETSPEDV GGMHAAVGIL TERGGMTSHA AVVARWWGKC 

       550        560        570        580        590        600 
CVSGCSGIRV NDAEKLVTIG SHVLREGEWL SLNGSTGEVI LGKQPLSPPA LSGDLGTFMA 

       610        620        630        640        650        660 
WVDDVRKLKV LANADTPDDA LTARNNGAQG IGLCRTEHMF FASDERIKAV RQMIMAPTLE 

       670        680        690        700        710        720 
LRQQALDRLL TYQRSDFEGI FRAMDGLPVT IRLLDHPSYE FLPEGNIEDI VSELCAETGA 

       730        740        750        760        770        780 
NQEDALARIE KLSEVNPMLG FRGCRLGISY PELTEMQARA IFEAAIAMTN QGVQVFPEIM 

       790        800        810        820        830        840 
VPLVGTPQEL GHQVTLIRQV AEKVFANVGK TIGYKVGTMI EIPRAALVAD EIAEQAEFFS 

       850        860        870        880        890        900 
FGTNDLTQMT FGYSRDDVGK FIPVHLAQGI LQHDPFEVLD QRGVGELVKF ATERGRKARP 

       910        920        930        940 
NLKVGICGEH GGEPSSVAFF AKAGLDFVSC SPFRVPIARL AAAQVLV

« Hide

Isoform 2 [UniParc].

Checksum: A8F7D316BE02D614
Show »

FASTA88395,982

References

[1]"Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence."
Matsuoka M., Ozeki Y., Yamamoto N., Hirano H., Kano-Murakami Y., Tanaka Y.
J. Biol. Chem. 263:11080-11083(1988) [PubMed: 2841317] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 71-89.
[2]"Structure, genetic mapping, and expression of the gene for pyruvate, orthophosphate dikinase from maize."
Matsuoka M.
J. Biol. Chem. 265:16772-16777(1990) [PubMed: 2170354] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Organ-specific transcripts of different size and abundance derive from the same pyruvate, orthophosphate dikinase gene in maize."
Glackin C.A., Grula J.W.
Proc. Natl. Acad. Sci. U.S.A. 87:3004-3008(1990) [PubMed: 2158100] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-75 (ISOFORM 1), ALTERNATIVE PROMOTER USAGE, TISSUE SPECIFICITY.
Strain: cv. B73.
[4]"Sequence of the phosphothreonyl regulatory site peptide from inactive maize leaf pyruvate, orthophosphate dikinase."
Roeske C.A., Kutny R.M., Budde R.J.A., Chollet R.
J. Biol. Chem. 263:6683-6687(1988) [PubMed: 2834385] [Abstract]
Cited for: PROTEIN SEQUENCE OF 521-535, PHOSPHORYLATION AT THR-527.
[5]"Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes."
Sheen J.
Plant Cell 3:225-245(1991) [PubMed: 1668653] [Abstract]
Cited for: PARTIAL NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), ALTERNATIVE PROMOTER USAGE, FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, INDUCTION.
[6]"Maize clones with putative DNA-binding activity."
Stapleton A.E., Walbot V.
Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 868-947.
Strain: cv. B73.
[7]"Cold lability of pyruvate, orthophosphate dikinase in the Maize Leaf."
Shirahashi K., Hayakawa S., Sugiyama T.
Plant Physiol. 62:826-830(1978) [PubMed: 16660615] [Abstract]
Cited for: ENZYME REGULATION.
[8]"Identification of the amino acid residues responsible for cold tolerance in Flaveria brownii pyruvate,orthophosphate dikinase."
Ohta S., Usami S., Ueki J., Kumashiro T., Komari T., Burnell J.N.
FEBS Lett. 403:5-9(1997) [PubMed: 9038349] [Abstract]
Cited for: BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, MUTAGENESIS OF LEU-946.
[9]"Site-directed mutagenesis of maize recombinant C4-pyruvate,orthophosphate dikinase at the phosphorylatable target threonine residue."
Chastain C.J., Lee M.E., Moorman M.A., Shameekumar P., Chollet R.
FEBS Lett. 413:169-173(1997) [PubMed: 9287137] [Abstract]
Cited for: MUTAGENESIS OF THR-527.
[10]"Further analysis of maize C(4) pyruvate,orthophosphate dikinase phosphorylation by its bifunctional regulatory protein using selective substitutions of the regulatory Thr-456 and catalytic His-458 residues."
Chastain C.J., Botschner M., Harrington G.E., Thompson B.J., Mills S.E., Sarath G., Chollet R.
Arch. Biochem. Biophys. 375:165-170(2000) [PubMed: 10683263] [Abstract]
Cited for: ENZYME REGULATION, ACTIVE SITE HIS-529, MUTAGENESIS OF THR-527 AND HIS-529.
[11]"Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion."
Nakanishi T., Nakatsu T., Matsuoka M., Sakata K., Kato H.
Biochemistry 44:1136-1144(2005) [PubMed: 15667207] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 72-947 IN APOPROTEIN AND IN COMPLEX WITH SUBSTRATE, ACTIVE SITE CYS-907, METAL BINDING AT GLU-821 AND ASP-845, SUBSTRATE BINDING AT ARG-635; ARG-692; ASN-844 AND ASP-845.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		J03901 mRNA. Translation: AAA33495.1. Frameshift.
M58656, M58655 Genomic DNA. Translation: AAA33498.1.
S46966 Genomic DNA. Translation: AAB23731.1.
S46965, S46964 Genomic DNA. Translation: AAB23730.1.
X14927 Genomic DNA. Translation: CAA33054.1.
AF152599 mRNA. Translation: AAD45281.1.
PIRKIZMPO. A29225.
PQ0190.
RefSeqNP_001105738.1. NM_001112268.1.
UniGeneZm.19489.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1VBGX-ray2.30A72-947[»]
1VBHX-ray2.30A72-947[»]
ProteinModelPortalP11155.
SMRP11155. Positions 74-947.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID542759.
KEGGzma:542759.

Organism-specific databases

GrameneP11155.
MaizeGDB25385.

Phylogenomic databases

GeneTreeEPGT00050000009059.

Enzyme and pathway databases

BRENDA2.7.9.1. 6752.

Family and domain databases

InterProIPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR008279. PEP-util_enz_mobile_dom.
IPR018274. PEP_util_AS.
IPR000121. PEP_util_C.
IPR023151. PEP_util_CS.
IPR002192. PPDK_PEP-bd.
IPR010121. Pyruvate_phosphate_dikinase.
IPR015813. Pyrv/PenolPyrv_Kinase.
[Graphical view]
Gene3DG3DSA:3.30.1490.20. ATP_grasp_subdomain_1. 2 hits.
G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit.
G3DSA:3.50.30.10. PEP_mobile. 1 hit.
G3DSA:3.20.20.60. Pyrv/PenolPyrv_Kinase_cat. 1 hit.
KOK01006.
PANTHERPTHR22931:SF9. PTHR22931:SF9. 1 hit.
PfamPF00391. PEP-utilizers. 1 hit.
PF02896. PEP-utilizers_C. 1 hit.
PF01326. PPDK_N. 1 hit.
[Graphical view]
PIRSFPIRSF000853. PPDK. 1 hit.
SUPFAMSSF52009. PEP_mobile. 1 hit.
SSF51621. Pyrv/PenolPyrv_Kinase_cat. 1 hit.
TIGRFAMsTIGR01828. Pyru_phos_dikin. 1 hit.
PROSITEPS00742. PEP_ENZYMES_2. 1 hit.
PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePPDK1_MAIZE
AccessionPrimary (citable) accession number: P11155
Secondary accession number(s): Q41846 expand/collapse secondary AC list , Q41847, Q42367, Q7DMU6, Q9XGW9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 2008
Last modified: November 16, 2011
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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