Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q5JCX3

- AMPPA_THEKO

UniProt

Q5JCX3 - AMPPA_THEKO

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

AMP phosphorylase

Gene

TK0352

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate.
CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate.
UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate.

Enzyme regulationi

AMP phosphorolysis is allosterically regulated by the substrate AMP.1 Publication

Kineticsi

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.

  1. KM=6.2 mM for CMP (in the presence of AMP, at 85 degrees Celsius)1 Publication
  2. KM=4.4 mM for UMP (in the presence of AMP, at 85 degrees Celsius)1 Publication
  3. KM=18.5 mM for GMP (in the presence of AMP, at 85 degrees Celsius)1 Publication
  4. KM=2.8 mM for phosphate (in the presence of AMP, at 85 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei168 – 1681AMP; via amide nitrogen
Binding sitei203 – 2031AMP; via amide nitrogen
Active sitei256 – 2561Proton donor1 Publication
Binding sitei264 – 2641AMP
Binding sitei288 – 2881AMP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi194 – 1996AMP

GO - Molecular functioni

  1. AMP binding Source: UniProtKB
  2. phosphate ion binding Source: UniProtKB
  3. phosphorylase activity Source: InterPro
  4. thymidine phosphorylase activity Source: InterPro
  5. transferase activity, transferring pentosyl groups Source: UniProtKB

GO - Biological processi

  1. AMP catabolic process Source: UniProtKB
  2. pyrimidine deoxyribonucleoside metabolic process Source: InterPro
  3. pyrimidine nucleobase metabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
AMP phosphorylase (EC:2.4.2.57)
Short name:
AMPpase
Alternative name(s):
Nucleoside monophosphate phosphorylase
Short name:
NMP phosphorylase
Gene namesi
Ordered Locus Names:TK0352
OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi256 – 2561D → N or A: Almost complete loss of activity. 1 Publication
Mutagenesisi288 – 2881K → A: Almost complete loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 503503AMP phosphorylasePRO_0000059093Add
BLAST

Expressioni

Inductioni

Constitutively expressed (at protein level). Does not respond to the addition of nucleosides.1 Publication

Interactioni

Subunit structurei

Forms an exceptionally large macromolecular structure (>40-mers) in solution.1 Publication

Protein-protein interaction databases

STRINGi69014.TK0352.

Structurei

Secondary structure

1
503
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87
Beta strandi16 – 194
Helixi21 – 277
Beta strandi34 – 418
Beta strandi43 – 519
Beta strandi58 – 625
Helixi63 – 664
Beta strandi76 – 816
Helixi87 – 959
Helixi102 – 11312
Helixi119 – 13214
Helixi136 – 14813
Beta strandi159 – 1657
Helixi174 – 18411
Beta strandi188 – 1936
Beta strandi197 – 2004
Helixi203 – 2075
Turni208 – 2103
Helixi217 – 22711
Beta strandi228 – 2347
Beta strandi237 – 2404
Helixi241 – 25313
Helixi258 – 27215
Beta strandi276 – 2849
Beta strandi287 – 2893
Helixi292 – 30817
Beta strandi312 – 3198
Beta strandi327 – 3293
Helixi330 – 34314
Helixi348 – 36417
Helixi373 – 38210
Helixi385 – 39612
Helixi405 – 4073
Beta strandi412 – 4187
Beta strandi420 – 4289
Helixi430 – 43910
Turni440 – 4445
Beta strandi445 – 4473
Beta strandi449 – 4524
Beta strandi465 – 4739
Helixi474 – 48714
Beta strandi490 – 4934

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4GA4X-ray3.51A/B85-503[»]
4GA5X-ray3.25A/B/C/D/E/F/G/H1-493[»]
4GA6X-ray2.21A/B1-493[»]
ProteinModelPortaliQ5JCX3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

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.1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0213.
HOGENOMiHOG000252767.
InParanoidiQ5JCX3.
KOiK00758.
OMAiLEWAFDE.

Family and domain databases

Gene3Di3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.
HAMAPiMF_02132. AMP_phosphorylase.
InterProiIPR017713. 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]
PANTHERiPTHR10515. PTHR10515. 1 hit.
PfamiPF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view]
PIRSFiPIRSF000478. TP_PyNP. 1 hit.
SMARTiSM00941. PYNP_C. 1 hit.
[Graphical view]
SUPFAMiSSF47648. SSF47648. 1 hit.
SSF52418. SSF52418. 1 hit.
SSF54680. SSF54680. 1 hit.
TIGRFAMsiTIGR03327. AMP_phos. 1 hit.
TIGR02645. ARCH_P_rylase. 1 hit.
PROSITEiPS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5JCX3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKAKIRILDM FSGRYTVLIN EEDAKEAKLH PDDLVKIEAG KKAVYGSVAL
60 70 80 90 100
SNLVGKGEVG ISRDVLDLHN FSEGETVSVI PAGTPESVRY IKKKMHGEKL
110 120 130 140 150
RKVEIEAIVR DIVDRKLRDI EISSFVTALE INGLDMDEIA ALTIAMAETG
160 170 180 190 200
DMLDIDRKPI MDVHSIGGVP GNKTNILVVP IVAAAGLTIP KTSSRAITSA
210 220 230 240 250
AGTADVVEVF ADVSFSLDEI KRIVEKVGAC LVWGGALNLA PADDITIKAE
260 270 280 290 300
RALSIDPTGL MLASIMSKKY AMGSQYVLID IPTGKGVKVE TVEEARSLAR
310 320 330 340 350
DFIELGKRLG QYVEVAITYG GQPIGHTVGP ALEAREALSA LMTGKGPGSL
360 370 380 390 400
IEKATGLAGI LLEMGGVAPA GTGKKMAKEI LESGKAWEKM KEIIEAQGGD
410 420 430 440 450
PNIKPEEIPI GDKTYTFTAA TSGYVTAIDN RAITAIARAA GAPEDKGAGI
460 470 480 490 500
ELYVKVGEKV KEGDPLFTIH AEHEARLDQA IVLARRTEPI RIEGMVLQRI

GNI
Length:503
Mass (Da):53,651
Last modified:February 15, 2005 - v1
Checksum:i63AB57AE279ACCBA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP006878 Genomic DNA. Translation: BAD84541.1.
RefSeqiYP_182765.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD84541; BAD84541; TK0352.
GeneIDi3235858.
KEGGitko:TK0352.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP006878 Genomic DNA. Translation: BAD84541.1 .
RefSeqi YP_182765.1. NC_006624.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4GA4 X-ray 3.51 A/B 85-503 [» ]
4GA5 X-ray 3.25 A/B/C/D/E/F/G/H 1-493 [» ]
4GA6 X-ray 2.21 A/B 1-493 [» ]
ProteinModelPortali Q5JCX3.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 69014.TK0352.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD84541 ; BAD84541 ; TK0352 .
GeneIDi 3235858.
KEGGi tko:TK0352.

Phylogenomic databases

eggNOGi COG0213.
HOGENOMi HOG000252767.
InParanoidi Q5JCX3.
KOi K00758.
OMAi LEWAFDE.

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-13274.
TKOD69014:GH72-358-MONOMER.

Family and domain databases

Gene3Di 3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.
HAMAPi MF_02132. AMP_phosphorylase.
InterProi IPR017713. 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 ]
PANTHERi PTHR10515. PTHR10515. 1 hit.
Pfami PF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view ]
PIRSFi PIRSF000478. TP_PyNP. 1 hit.
SMARTi SM00941. PYNP_C. 1 hit.
[Graphical view ]
SUPFAMi SSF47648. SSF47648. 1 hit.
SSF52418. SSF52418. 1 hit.
SSF54680. SSF54680. 1 hit.
TIGRFAMsi TIGR03327. AMP_phos. 1 hit.
TIGR02645. ARCH_P_rylase. 1 hit.
PROSITEi PS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiAMPPA_THEKO
AccessioniPrimary (citable) accession number: Q5JCX3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: February 15, 2005
Last modified: October 29, 2014
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3