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P22983 (PPDK_CLOSY) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pyruvate, phosphate dikinase
EC=2.7.9.1
Alternative name(s):
Pyruvate, orthophosphate dikinase
Gene names
Name:ppdK
OrganismClostridium symbiosum (Bacteroides symbiosus)
Taxonomic identifier1512 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length874 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.

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 By similarity.

Subunit structure

Homodimer.

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-453 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme By similarity.

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.

Sequence similarities

Belongs to the PEP-utilizing enzyme family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1
Chain2 – 874873Pyruvate, phosphate dikinase
PRO_0000147046

Regions

Region2 – 340339N-terminal
Region340 – 39960Linker 1
Region400 – 49899Central
Region499 – 53335Linker 2
Region534 – 874341C-terminal

Sites

Active site4551Tele-phosphohistidine intermediate Ref.6
Active site8311Proton donor Probable
Metal binding7451Magnesium
Metal binding7691Magnesium
Binding site921ATP Potential
Binding site5611Substrate
Binding site6171Substrate
Binding site7451Substrate
Binding site7661Substrate; via carbonyl oxygen
Binding site7671Substrate; via amide nitrogen
Binding site7681Substrate
Binding site7691Substrate; via amide nitrogen

Amino acid modifications

Modified residue4531Phosphothreonine; by PDRP1 By similarity

Experimental info

Mutagenesis8311C → A: Lack of phosphotransfer activity. Ref.4
Sequence conflict941G → A in AAA22917. Ref.1
Sequence conflict5151A → R in AAA22917. Ref.1
Sequence conflict836 – 87439GDPSS…ALNNK → EILLP in AAA22917. Ref.1

Secondary structure

1 .................................................................................................................................................................... 874
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P22983 [UniParc].

Last modified January 23, 2007. Version 5.
Checksum: 13C1918807DEA36C

FASTA87496,654
        10         20         30         40         50         60 
MAKWVYKFEE GNASMRNLLG GKGCNLAEMT ILGMPIPQGF TVTTEACTEY YNSGKQITQE 

        70         80         90        100        110        120 
IQDQIFEAIT WLEELNGKKF GDTEDPLLVS VRSGARASMP GMMDTILNLG LNDVAVEGFA 

       130        140        150        160        170        180 
KKTGNPRFAY DSYRRFIQMY SDVVMEVPKS HFEKIIDAMK EEKGVHFDTD LTADDLKELA 

       190        200        210        220        230        240 
EKFKAVYKEA MNGEEFPQEP KDQLMGAVKA VFRSWDNPRA IVYRRMNDIP GDWGTAVNVQ 

       250        260        270        280        290        300 
TMVFGNKGET SGTGVAFTRN PSTGEKGIYG EYLINAQGED VVAGVRTPQP ITQLENDMPD 

       310        320        330        340        350        360 
CYKQFMDLAM KLEKHFRDMQ DMEFTIEEGK LYFLQTRNGK RTAPAALQIA CDLVDEGMIT 

       370        380        390        400        410        420 
EEEAVVRIEA KSLDQLLHPT FNPAALKAGE VIGSALPASP GAAAGKVYFT ADEAKAAHEK 

       430        440        450        460        470        480 
GERVILVRLE TSPEDIEGMH AAEGILTVRG GMTSHAAVVA RGMGTCCVSG CGEIKINEEA 

       490        500        510        520        530        540 
KTFELGGHTF AEGDYISLDG STGKIYKGDI ETQEASVSGS FERIMVWADK FRTLKVRTNA 

       550        560        570        580        590        600 
DTPEDTLNAV KLGAEGIGLC RTEHMFFEAD RIMKIRKMIL SDSVEAREEA LNELIPFQKG 

       610        620        630        640        650        660 
DFKAMYKALE GRPMTVRYLD PPLHEFVPHT EEEQAELAKN MGLTLAEVKA KVDELHEFNP 

       670        680        690        700        710        720 
MMGHRGCRLA VTYPEIAKMQ TRAVMEAAIE VKEETGIDIV PEIMIPLVGE KKELKFVKDV 

       730        740        750        760        770        780 
VVEVAEQVKK EKGSDMQYHI GTMIEIPRAA LTADAIAEEA EFFSFGTNDL TQMTFGFSRD 

       790        800        810        820        830        840 
DAGKFLDSYY KAKIYESDPF ARLDQTGVGQ LVEMAVKKGR QTRPGLKCGI CGEHGGDPSS 

       850        860        870 
VEFCHKVGLN YVSCSPFRVP IARLAAAQAA LNNK

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References

[1]"Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs."
Pocalyko D.J., Carroll L.J., Martin B.M., Babbitt P.C., Dunaway-Mariano D.
Biochemistry 29:10757-10765(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11; 56-70; 128-134; 226-243; 372-386; 407-415; 652-664 AND 693-702.
[2]Dunaway-Mariano D., Ye D.
Submitted (SEP-2000) to UniProtKB
Cited for: SEQUENCE REVISION TO 94.
[3]"Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier."
Goss N.H., Evans C.T., Wood H.G.
Biochemistry 19:5805-5809(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 451-462.
[4]"Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with [1-14C]bromopyruvate and site-directed mutagenesis."
Xu Y., Yankie L., Shen L., Jung Y.S., Mariano P.S., Dunaway-Mariano D., Martin B.M.
Biochemistry 34:2181-2187(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: ACTIVE SITE CYS-831, MUTAGENESIS OF CYS-831.
[5]"Investigation of the role of the domain linkers in separate site catalysis by Clostridium symbiosum pyruvate phosphate dikinase."
Wei M., Ye D., Dunaway-Mariano D.
Biochemistry 40:13466-13473(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE.
[6]"Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase."
Ye D., Wei M., McGuire M., Huang K., Kapadia G., Herzberg O., Martin B.M., Dunaway-Mariano D.
J. Biol. Chem. 276:37630-37639(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), ACTIVE SITE HIS-455.
[7]"Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites."
Herzberg O., Cheng C.C.H., Kapadia G., McGuire M., Carroll L.J., Noh S.J., Dunaway-Mariano D.
Proc. Natl. Acad. Sci. U.S.A. 93:2652-2657(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SEQUENCE REVISION, ACTIVE SITE CYS-831, SUBSTRATE BINDING AT ARG-561; ARG-617; GLU-745; GLY-766; THR-767; ASN-768 AND ASP-769, METAL BINDING AT GLU-745 AND ASP-769.
[8]"Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase."
McGuire M., Huang K., Kapadia G., Herzberg O., Dunaway-Mariano D.
Biochemistry 37:13463-13474(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Strain: JM101.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M60920 mRNA. Translation: AAA22917.1.
PIRKIQAPO. A36231.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DIKX-ray2.30A1-874[»]
1GGOX-ray2.60A2-873[»]
1JDEX-ray2.80A2-874[»]
1KBLX-ray1.94A2-873[»]
1KC7X-ray2.20A2-873[»]
2DIKX-ray2.50A2-874[»]
2FM4NMR-A384-510[»]
2R82X-ray3.60A1-874[»]
ProteinModelPortalP22983.
SMRP22983. Positions 2-873.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP22983.

Family and domain databases

Gene3D3.20.20.60. 1 hit.
3.30.1490.20. 2 hits.
3.30.470.20. 1 hit.
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]
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...

Other

EvolutionaryTraceP22983.

Entry information

Entry namePPDK_CLOSY
AccessionPrimary (citable) accession number: P22983
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: January 23, 2007
Last modified: April 3, 2013
This is version 104 of the entry and version 5 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents