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Q5JCX3 (AMPPA_THEKO) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 74. Feed History...

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

Names and origin

Protein namesRecommended name:
AMP phosphorylase

Short name=AMPpase
EC=2.4.2.57
Alternative name(s):
Nucleoside monophosphate phosphorylase
Short name=NMP phosphorylase
Gene names
Ordered Locus Names:TK0352
OrganismThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]
Taxonomic identifier69014 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus

Protein attributes

Sequence length503 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the conversion of AMP and phosphate to adenine and ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward CMP, dCMP and UMP in addition to AMP. Functions in an archaeal AMP degradation pathway, together with R15P isomerase and RubisCO. Ref.2 Ref.3

Catalytic activity

AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate. Ref.2 Ref.3

CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate. Ref.2 Ref.3

UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate. Ref.2 Ref.3

Enzyme regulation

AMP phosphorolysis is allosterically regulated by the substrate AMP. Ref.3

Subunit structure

Forms an exceptionally large macromolecular structure (>40-mers) in solution. Ref.4

Induction

Constitutively expressed (at protein level). Does not respond to the addition of nucleosides. Ref.3

Domain

The N-terminal domain (residues 1-84), characteristic of archaeal AMPpases, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Harbors two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain; these two interactions can continuously occur in a repetitive manner, leading to multimerization. Ref.4

Sequence similarities

Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family. Type 2 subfamily.

Biophysicochemical properties

Kinetic parameters:

kcat is 39.1 sec(-1), 15.0 sec(-1), 10.5 sec(-1) and 2.7 sec(-1), with CMP, AMP, UMP, and GMP as substrate, respectively (at 85 degrees Celsius). KM for AMP was not determined because the reaction does not follow Michaelis-Menten kinetics.

KM=6.2 mM for CMP (in the presence of AMP, at 85 degrees Celsius) Ref.3

KM=4.4 mM for UMP (in the presence of AMP, at 85 degrees Celsius)

KM=18.5 mM for GMP (in the presence of AMP, at 85 degrees Celsius)

KM=2.8 mM for phosphate (in the presence of AMP, at 85 degrees Celsius)

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 503503AMP phosphorylase HAMAP-Rule MF_00703
PRO_0000059093

Regions

Nucleotide binding194 – 1996AMP HAMAP-Rule MF_00703

Sites

Active site2561Proton donor Probable
Binding site1681AMP; via amide nitrogen
Binding site2031AMP; via amide nitrogen
Binding site2641AMP
Binding site2881AMP

Experimental info

Mutagenesis2561D → N or A: Almost complete loss of activity. Ref.4
Mutagenesis2881K → A: Almost complete loss of activity. Ref.4

Secondary structure

............................................................................. 503
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q5JCX3 [UniParc].

Last modified February 15, 2005. Version 1.
Checksum: 63AB57AE279ACCBA

FASTA50353,651
        10         20         30         40         50         60 
MKAKIRILDM FSGRYTVLIN EEDAKEAKLH PDDLVKIEAG KKAVYGSVAL SNLVGKGEVG 

        70         80         90        100        110        120 
ISRDVLDLHN FSEGETVSVI PAGTPESVRY IKKKMHGEKL RKVEIEAIVR DIVDRKLRDI 

       130        140        150        160        170        180 
EISSFVTALE INGLDMDEIA ALTIAMAETG DMLDIDRKPI MDVHSIGGVP GNKTNILVVP 

       190        200        210        220        230        240 
IVAAAGLTIP KTSSRAITSA AGTADVVEVF ADVSFSLDEI KRIVEKVGAC LVWGGALNLA 

       250        260        270        280        290        300 
PADDITIKAE RALSIDPTGL MLASIMSKKY AMGSQYVLID IPTGKGVKVE TVEEARSLAR 

       310        320        330        340        350        360 
DFIELGKRLG QYVEVAITYG GQPIGHTVGP ALEAREALSA LMTGKGPGSL IEKATGLAGI 

       370        380        390        400        410        420 
LLEMGGVAPA GTGKKMAKEI LESGKAWEKM KEIIEAQGGD PNIKPEEIPI GDKTYTFTAA 

       430        440        450        460        470        480 
TSGYVTAIDN RAITAIARAA GAPEDKGAGI ELYVKVGEKV KEGDPLFTIH AEHEARLDQA 

       490        500 
IVLARRTEPI RIEGMVLQRI GNI 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]"Archaeal type III RuBisCOs function in a pathway for AMP metabolism."
Sato T., Atomi H., Imanaka T.
Science 315:1003-1006(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, PATHWAY.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[3]"Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway."
Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T., Atomi H.
J. Bacteriol. 194:6847-6855(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME REGULATION, KINETIC PARAMETERS, INDUCTION, PATHWAY.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[4]"Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization."
Nishitani Y., Aono R., Nakamura A., Sato T., Atomi H., Imanaka T., Miki K.
J. Mol. Biol. 425:2709-2721(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH SUBSTRATE, SUBUNIT, DOMAIN, ACTIVE SITE, MUTAGENESIS OF ASP-256 AND LYS-288.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP006878 Genomic DNA. Translation: BAD84541.1.
RefSeqYP_182765.1. NC_006624.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4GA4X-ray3.51A/B85-503[»]
4GA5X-ray3.25A/B/C/D/E/F/G/H1-493[»]
4GA6X-ray2.21A/B1-493[»]
ProteinModelPortalQ5JCX3.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING69014.TK0352.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD84541; BAD84541; TK0352.
GeneID3235858.
KEGGtko:TK0352.

Phylogenomic databases

eggNOGCOG0213.
HOGENOMHOG000252767.
KOK00758.
OMALEWAFDE.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-13274.
TKOD69014:GH72-358-MONOMER.

Family and domain databases

Gene3D3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.
HAMAPMF_02132. AMP_phosphorylase.
InterProIPR017713. AMP_phosphorylase.
IPR000312. Glycosyl_Trfase_fam3.
IPR017459. Glycosyl_Trfase_fam3_N_dom.
IPR013102. PYNP_C.
IPR000053. Pyrmidine_PPase.
IPR017872. Pyrmidine_PPase_CS.
IPR013466. Thymidine/AMP_Pase.
[Graphical view]
PANTHERPTHR10515. PTHR10515. 1 hit.
PfamPF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view]
PIRSFPIRSF000478. TP_PyNP. 1 hit.
SMARTSM00941. PYNP_C. 1 hit.
[Graphical view]
SUPFAMSSF47648. SSF47648. 1 hit.
SSF52418. SSF52418. 1 hit.
SSF54680. SSF54680. 1 hit.
TIGRFAMsTIGR03327. AMP_phos. 1 hit.
TIGR02645. ARCH_P_rylase. 1 hit.
PROSITEPS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameAMPPA_THEKO
AccessionPrimary (citable) accession number: Q5JCX3
Entry history
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: February 15, 2005
Last modified: July 9, 2014
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references