AMPPA_THEKO
ID AMPPA_THEKO Reviewed; 503 AA.
AC Q5JCX3;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=AMP phosphorylase {ECO:0000255|HAMAP-Rule:MF_02132};
DE Short=AMPpase {ECO:0000255|HAMAP-Rule:MF_02132};
DE EC=2.4.2.57 {ECO:0000255|HAMAP-Rule:MF_02132, ECO:0000269|PubMed:17303759, ECO:0000269|PubMed:23065974};
DE AltName: Full=Nucleoside monophosphate phosphorylase {ECO:0000255|HAMAP-Rule:MF_02132};
DE Short=NMP phosphorylase {ECO:0000255|HAMAP-Rule:MF_02132};
GN Name=deoA {ECO:0000303|PubMed:17303759}; OrderedLocusNames=TK0352;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=17303759; DOI=10.1126/science.1135999;
RA Sato T., Atomi H., Imanaka T.;
RT "Archaeal type III RuBisCOs function in a pathway for AMP metabolism.";
RL Science 315:1003-1006(2007).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP KINETIC PARAMETERS, INDUCTION, AND PATHWAY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=23065974; DOI=10.1128/jb.01335-12;
RA Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T.,
RA Atomi H.;
RT "Enzymatic characterization of AMP phosphorylase and ribose-1,5-
RT bisphosphate isomerase functioning in an archaeal AMP metabolic pathway.";
RL J. Bacteriol. 194:6847-6855(2012).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP SUBSTRATE, SUBUNIT, DOMAIN, ACTIVE SITE, AND MUTAGENESIS OF ASP-256 AND
RP LYS-288.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=23659790; DOI=10.1016/j.jmb.2013.04.026;
RA Nishitani Y., Aono R., Nakamura A., Sato T., Atomi H., Imanaka T., Miki K.;
RT "Structure analysis of archaeal AMP phosphorylase reveals two unique modes
RT of dimerization.";
RL J. Mol. Biol. 425:2709-2721(2013).
CC -!- FUNCTION: Catalyzes the conversion of AMP and phosphate to adenine and
CC ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward
CC CMP, dCMP and UMP in addition to AMP. Functions in an archaeal AMP
CC degradation pathway, together with R15P isomerase and RubisCO.
CC {ECO:0000269|PubMed:17303759, ECO:0000269|PubMed:23065974}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate;
CC Xref=Rhea:RHEA:36975, ChEBI:CHEBI:16708, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:68688, ChEBI:CHEBI:456215; EC=2.4.2.57;
CC Evidence={ECO:0000269|PubMed:17303759, ECO:0000269|PubMed:23065974};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=CMP + phosphate = alpha-D-ribose 1,5-bisphosphate + cytosine;
CC Xref=Rhea:RHEA:36987, ChEBI:CHEBI:16040, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:60377, ChEBI:CHEBI:68688; EC=2.4.2.57;
CC Evidence={ECO:0000269|PubMed:23065974};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + UMP = alpha-D-ribose 1,5-bisphosphate + uracil;
CC Xref=Rhea:RHEA:36991, ChEBI:CHEBI:17568, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57865, ChEBI:CHEBI:68688; EC=2.4.2.57;
CC Evidence={ECO:0000269|PubMed:23065974};
CC -!- ACTIVITY REGULATION: AMP phosphorolysis is allosterically regulated by
CC the substrate AMP. {ECO:0000269|PubMed:23065974}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.2 mM for CMP (in the presence of AMP, at 85 degrees Celsius)
CC {ECO:0000269|PubMed:23065974};
CC KM=4.4 mM for UMP (in the presence of AMP, at 85 degrees Celsius)
CC {ECO:0000269|PubMed:23065974};
CC KM=18.5 mM for GMP (in the presence of AMP, at 85 degrees Celsius)
CC {ECO:0000269|PubMed:23065974};
CC KM=2.8 mM for phosphate (in the presence of AMP, at 85 degrees
CC Celsius) {ECO:0000269|PubMed:23065974};
CC Note=kcat is 39.1 sec(-1), 15.0 sec(-1), 10.5 sec(-1) and 2.7 sec(-
CC 1), with CMP, AMP, UMP, and GMP as substrate, respectively (at 85
CC degrees Celsius). KM for AMP was not determined because the reaction
CC does not follow Michaelis-Menten kinetics.
CC {ECO:0000269|PubMed:23065974};
CC -!- SUBUNIT: Forms an exceptionally large macromolecular structure (>40-
CC mers) in solution. {ECO:0000269|PubMed:23659790}.
CC -!- INDUCTION: Constitutively expressed (at protein level). Does not
CC respond to the addition of nucleosides. {ECO:0000269|PubMed:23065974}.
CC -!- DOMAIN: The N-terminal domain (residues 1-84), characteristic of
CC archaeal AMPpases, is essential for enzymatic activity, participating
CC in multimerization as well as domain closure of the active site upon
CC substrate binding. Harbors two dimer interfaces within a single
CC molecule: one by the central domain and the other by the C-terminal
CC domain; these two interactions can continuously occur in a repetitive
CC manner, leading to multimerization. {ECO:0000269|PubMed:23659790}.
CC -!- SIMILARITY: Belongs to the thymidine/pyrimidine-nucleoside
CC phosphorylase family. Type 2 subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_02132}.
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DR EMBL; AP006878; BAD84541.1; -; Genomic_DNA.
DR RefSeq; WP_011249307.1; NC_006624.1.
DR PDB; 4GA4; X-ray; 3.51 A; A/B=85-503.
DR PDB; 4GA5; X-ray; 3.25 A; A/B/C/D/E/F/G/H=1-493.
DR PDB; 4GA6; X-ray; 2.21 A; A/B=1-493.
DR PDBsum; 4GA4; -.
DR PDBsum; 4GA5; -.
DR PDBsum; 4GA6; -.
DR AlphaFoldDB; Q5JCX3; -.
DR SMR; Q5JCX3; -.
DR STRING; 69014.TK0352; -.
DR EnsemblBacteria; BAD84541; BAD84541; TK0352.
DR GeneID; 3235858; -.
DR KEGG; tko:TK0352; -.
DR PATRIC; fig|69014.16.peg.349; -.
DR eggNOG; arCOG02013; Archaea.
DR HOGENOM; CLU_025040_6_0_2; -.
DR InParanoid; Q5JCX3; -.
DR OMA; DVWRRMI; -.
DR OrthoDB; 43931at2157; -.
DR PhylomeDB; Q5JCX3; -.
DR BioCyc; MetaCyc:MON-13274; -.
DR BRENDA; 2.4.2.57; 5246.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004645; F:1,4-alpha-oligoglucan phosphorylase activity; IEA:InterPro.
DR GO; GO:0016208; F:AMP binding; IDA:UniProtKB.
DR GO; GO:0016763; F:pentosyltransferase activity; IDA:UniProtKB.
DR GO; GO:0042301; F:phosphate ion binding; IDA:UniProtKB.
DR GO; GO:0006196; P:AMP catabolic process; IDA:UniProtKB.
DR GO; GO:0046125; P:pyrimidine deoxyribonucleoside metabolic process; IEA:InterPro.
DR GO; GO:0006206; P:pyrimidine nucleobase metabolic process; IEA:InterPro.
DR Gene3D; 3.40.1030.10; -; 1.
DR Gene3D; 3.90.1170.30; -; 1.
DR HAMAP; MF_02132; AMP_phosphorylase; 1.
DR InterPro; IPR017713; AMP_phosphorylase.
DR InterPro; IPR000312; Glycosyl_Trfase_fam3.
DR InterPro; IPR017459; Glycosyl_Trfase_fam3_N_dom.
DR InterPro; IPR036320; Glycosyl_Trfase_fam3_N_dom_sf.
DR InterPro; IPR035902; Nuc_phospho_transferase.
DR InterPro; IPR036566; PYNP-like_C_sf.
DR InterPro; IPR013102; PYNP_C.
DR InterPro; IPR017872; Pyrmidine_PPase_CS.
DR InterPro; IPR013466; Thymidine/AMP_Pase.
DR InterPro; IPR000053; Thymidine/pyrmidine_PPase.
DR PANTHER; PTHR10515; PTHR10515; 1.
DR Pfam; PF02885; Glycos_trans_3N; 1.
DR Pfam; PF00591; Glycos_transf_3; 1.
DR Pfam; PF07831; PYNP_C; 1.
DR PIRSF; PIRSF000478; TP_PyNP; 1.
DR SMART; SM00941; PYNP_C; 1.
DR SUPFAM; SSF47648; SSF47648; 1.
DR SUPFAM; SSF52418; SSF52418; 1.
DR SUPFAM; SSF54680; SSF54680; 1.
DR TIGRFAMs; TIGR03327; AMP_phos; 1.
DR TIGRFAMs; TIGR02645; ARCH_P_rylase; 1.
DR PROSITE; PS00647; THYMID_PHOSPHORYLASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; Glycosyltransferase; Reference proteome;
KW Transferase.
FT CHAIN 1..503
FT /note="AMP phosphorylase"
FT /id="PRO_0000059093"
FT ACT_SITE 256
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:23659790"
FT BINDING 168
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:23659790"
FT BINDING 194..199
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:23659790"
FT BINDING 203
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:23659790"
FT BINDING 264
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:23659790"
FT BINDING 288
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:23659790"
FT MUTAGEN 256
FT /note="D->N,A: Almost complete loss of activity."
FT /evidence="ECO:0000269|PubMed:23659790"
FT MUTAGEN 288
FT /note="K->A: Almost complete loss of activity."
FT /evidence="ECO:0000269|PubMed:23659790"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 21..27
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 34..41
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 43..51
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 58..62
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 87..95
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 102..113
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 119..132
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 136..148
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 159..165
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 174..184
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 188..193
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 203..207
FT /evidence="ECO:0007829|PDB:4GA6"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 217..227
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 228..234
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 237..240
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 241..253
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 258..272
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 276..284
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 287..289
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 292..308
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 312..319
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 327..329
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 330..343
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 348..364
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 373..382
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 385..396
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 405..407
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 412..418
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 420..428
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 430..439
FT /evidence="ECO:0007829|PDB:4GA6"
FT TURN 440..444
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 445..447
FT /evidence="ECO:0007829|PDB:4GA5"
FT STRAND 449..452
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 465..473
FT /evidence="ECO:0007829|PDB:4GA6"
FT HELIX 474..487
FT /evidence="ECO:0007829|PDB:4GA6"
FT STRAND 490..493
FT /evidence="ECO:0007829|PDB:4GA6"
SQ SEQUENCE 503 AA; 53651 MW; 63AB57AE279ACCBA CRC64;
MKAKIRILDM FSGRYTVLIN EEDAKEAKLH PDDLVKIEAG KKAVYGSVAL SNLVGKGEVG
ISRDVLDLHN FSEGETVSVI PAGTPESVRY IKKKMHGEKL RKVEIEAIVR DIVDRKLRDI
EISSFVTALE INGLDMDEIA ALTIAMAETG DMLDIDRKPI MDVHSIGGVP GNKTNILVVP
IVAAAGLTIP KTSSRAITSA AGTADVVEVF ADVSFSLDEI KRIVEKVGAC LVWGGALNLA
PADDITIKAE RALSIDPTGL MLASIMSKKY AMGSQYVLID IPTGKGVKVE TVEEARSLAR
DFIELGKRLG QYVEVAITYG GQPIGHTVGP ALEAREALSA LMTGKGPGSL IEKATGLAGI
LLEMGGVAPA GTGKKMAKEI LESGKAWEKM KEIIEAQGGD PNIKPEEIPI GDKTYTFTAA
TSGYVTAIDN RAITAIARAA GAPEDKGAGI ELYVKVGEKV KEGDPLFTIH AEHEARLDQA
IVLARRTEPI RIEGMVLQRI GNI
