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SAMP-activating enzyme E1 (EC 2.7.7.-) (Ubiquitin-like activating enzyme of archaea) (Ubl-activating enzyme)

 UBAA_HALVD              Reviewed;         270 AA.
D4GSF3;
10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
18-MAY-2010, sequence version 1.
16-JAN-2019, entry version 49.
RecName: Full=SAMP-activating enzyme E1;
EC=2.7.7.-;
AltName: Full=Ubiquitin-like activating enzyme of archaea;
Short=Ubl-activating enzyme;
Name=ubaA; OrderedLocusNames=HVO_0558;
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC
14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii).
Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria;
Haloferacales; Haloferacaceae; Haloferax.
NCBI_TaxID=309800;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 /
VKM B-1768 / DS2;
PubMed=20333302; DOI=10.1371/journal.pone.0009605;
Hartman A.L., Norais C., Badger J.H., Delmas S., Haldenby S.,
Madupu R., Robinson J., Khouri H., Ren Q., Lowe T.M.,
Maupin-Furlow J., Pohlschroder M., Daniels C., Pfeiffer F., Allers T.,
Eisen J.A.;
"The complete genome sequence of Haloferax volcanii DS2, a model
archaeon.";
PLoS ONE 5:E9605-E9605(2010).
[2]
SAMPYLATION AT LYS-113, AND IDENTIFICATION BY MASS SPECTROMETRY.
STRAIN=ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 /
VKM B-1768 / DS2;
PubMed=20054389; DOI=10.1038/nature08659;
Humbard M.A., Miranda H.V., Lim J.M., Krause D.J., Pritz J.R.,
Zhou G., Chen S., Wells L., Maupin-Furlow J.A.;
"Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax
volcanii.";
Nature 463:54-60(2010).
[3]
FUNCTION, ACTIVE SITE, MUTAGENESIS OF CYS-188, AND DISRUPTION
PHENOTYPE.
STRAIN=DS2 / DS70;
PubMed=21368171; DOI=10.1073/pnas.1018151108;
Miranda H.V., Nembhard N., Su D., Hepowit N., Krause D.J., Pritz J.R.,
Phillips C., Soll D., Maupin-Furlow J.A.;
"E1- and ubiquitin-like proteins provide a direct link between protein
conjugation and sulfur transfer in archaea.";
Proc. Natl. Acad. Sci. U.S.A. 108:4417-4422(2011).
[4]
FUNCTION.
STRAIN=DS2 / DS70;
PubMed=24097257; DOI=10.1074/mcp.M113.029652;
Miranda H.V., Antelmann H., Hepowit N., Chavarria N.E., Krause D.J.,
Pritz J.R., Basell K., Becher D., Humbard M.A., Brocchieri L.,
Maupin-Furlow J.A.;
"Archaeal ubiquitin-like SAMP3 is isopeptide-linked to proteins via a
UbaA-dependent mechanism.";
Mol. Cell. Proteomics 13:220-239(2014).
-!- FUNCTION: Likely activates multiple ubiquitin-like SAMPs for
protein conjugation as well as for sulfur transfer, via ATP-
dependent adenylation at their C-terminus. In fact, it is required
for the formation of all three SAMP1-, SAMP2- and SAMP3-protein
conjugates, and for molybdenum cofactor (MoCo) biosynthesis and
thiolation of tRNAs. {ECO:0000269|PubMed:21368171,
ECO:0000269|PubMed:24097257}.
-!- CATALYTIC ACTIVITY:
Reaction=[small archaeal modifier protein]-C-terminal Gly-Gly +
ATP + H(+) = [small archaeal modifier protein]-C-terminal Gly-
Gly-AMP + diphosphate; Xref=Rhea:RHEA:56100, Rhea:RHEA-
COMP:14381, Rhea:RHEA-COMP:14383, ChEBI:CHEBI:15378,
ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:90618,
ChEBI:CHEBI:90778;
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
Note=Binds 1 zinc ion per subunit. {ECO:0000250};
-!- PTM: Sampylated at Lys-113 with the archaeal ubiquitin-like
protein SAMP2. Also sampylated with SAMP1.
{ECO:0000269|PubMed:20054389}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene are deficient in
sampylation, i.e. SAMP-protein conjugates. Moreover, they do not
grow anaerobically with DMSO and do not show DMSO reductase
activity, but their growth in the presence of oxygen is not
affected; however, they are retarded in aerobic growth at 50
degrees Celsius. The lysine tRNAs of the mutant strain appear to
be nonthiolated. {ECO:0000269|PubMed:21368171}.
-!- SIMILARITY: Belongs to the HesA/MoeB/ThiF family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; CP001956; ADE04227.1; -; Genomic_DNA.
RefSeq; WP_004044375.1; NZ_AOHU01000098.1.
SMR; D4GSF3; -.
STRING; 309800.HVO_0558; -.
EnsemblBacteria; ADE04227; ADE04227; HVO_0558.
GeneID; 8925734; -.
KEGG; hvo:HVO_0558; -.
eggNOG; arCOG01676; Archaea.
eggNOG; COG0476; LUCA.
HOGENOM; HOG000281217; -.
KO; K22837; -.
OMA; YSRHVIM; -.
OrthoDB; 86909at2157; -.
BioCyc; MetaCyc:MONOMER-20239; -.
Proteomes; UP000008243; Chromosome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0016779; F:nucleotidyltransferase activity; IEA:UniProtKB-KW.
GO; GO:0008641; F:ubiquitin-like modifier activating enzyme activity; IEA:InterPro.
InterPro; IPR000594; ThiF_NAD_FAD-bd.
InterPro; IPR035985; Ubiquitin-activating_enz.
Pfam; PF00899; ThiF; 1.
SUPFAM; SSF69572; SSF69572; 1.
1: Evidence at protein level;
ATP-binding; Complete proteome; Isopeptide bond; Metal-binding;
Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
Thioester bond; Transferase; Ubl conjugation; Zinc.
CHAIN 1 270 SAMP-activating enzyme E1.
/FTId=PRO_0000397107.
NP_BIND 70 74 ATP. {ECO:0000250}.
NP_BIND 131 132 ATP. {ECO:0000250}.
ACT_SITE 188 188 Glycyl thioester intermediate.
{ECO:0000305|PubMed:21368171}.
METAL 171 171 Zinc. {ECO:0000250}.
METAL 174 174 Zinc. {ECO:0000250}.
METAL 245 245 Zinc. {ECO:0000250}.
METAL 248 248 Zinc. {ECO:0000250}.
BINDING 42 42 ATP; via amide nitrogen. {ECO:0000250}.
BINDING 63 63 ATP. {ECO:0000250}.
BINDING 87 87 ATP. {ECO:0000250}.
CROSSLNK 113 113 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SAMP2).
MUTAGEN 188 188 C->S: Loss of activity since this mutant
is not able to complement a ubaA deletion
in trans to restore sampylation and tRNA
thiolation.
{ECO:0000269|PubMed:21368171}.
SEQUENCE 270 AA; 28704 MW; B9DFDCD37024FA32 CRC64;
MTLSLDATQL DRYSRHIIMD EVGPEGQGRL LSSRVVVVGA GGLGAPAIQY LAAVGVGELV
VVDDDVVERS NLQRQVVHCD DDVGTPKAES AAAFVRGLNP DVSVEPVEAR VDKSNVHEVV
AGSDVVVDAS DNFPTRYLLN DVCRFEGIPL VHGAIYKFEG QATTLVPDGP CYRCLFPEAP
EPGTVPDCAT TGVLGVLPGT VGCIQATEAM KLLLDEGEAL DGRLLFYDAM DMTFETVPYR
TNPDCPVCGE GGVDSIEDID YVESCAISLD


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Pathways :
WP142: mRNA processing
WP1493: Carbon assimilation C4 pathway
WP2340: Thiamine (vitamin B1) biosynthesis and salvage
WP2341: vitamin B1 (thiamin) biosynthesis and salvage pathway
WP2344: vitamin B6 (pyridoxine, pyridoxal, pyridoxamine) biosynthesis and salvage pathway
WP2349: vitamin B3 (niacin), NAD and NADP biosynthesis pathway
WP626: Abscisic Acid Biosynthesis
WP211: BMP signaling pathway
WP2199: Seed Development
WP2292: Chemokine signaling pathway
WP2359: Parkin-Ubiquitin Proteasomal System pathway

Related Genes :
[UBA3 UBE1C] NEDD8-activating enzyme E1 catalytic subunit (EC 6.2.1.-) (NEDD8-activating enzyme E1C) (Ubiquitin-activating enzyme E1C) (Ubiquitin-like modifier-activating enzyme 3) (Ubiquitin-activating enzyme 3)
[ATG7 APG7L] Ubiquitin-like modifier-activating enzyme ATG7 (ATG12-activating enzyme E1 ATG7) (Autophagy-related protein 7) (APG7-like) (hAGP7) (Ubiquitin-activating enzyme E1-like protein)
[Atg7 Apg7l] Ubiquitin-like modifier-activating enzyme ATG7 (ATG12-activating enzyme E1 ATG7) (Autophagy-related protein 7) (APG7-like) (mAGP7) (Ubiquitin-activating enzyme E1-like protein)
[ATG7 APG7 CVT2 YHR171W] Ubiquitin-like modifier-activating enzyme ATG7 (ATG12-activating enzyme E1 ATG7) (Autophagy-related protein 7) (Cytoplasm to vacuole targeting protein 2)
[Atg7 Apg7l] Ubiquitin-like modifier-activating enzyme ATG7 (ATG12-activating enzyme E1 ATG7) (Autophagy-related protein 7) (APG7-like)
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[UBC7 QRI8 YMR022W YM9711.12] Ubiquitin-conjugating enzyme E2 7 (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme 7) (Ubiquitin carrier protein) (Ubiquitin-conjugating enzyme E2-18 kDa) (Ubiquitin-protein ligase)
[CDC34 UBCH3 UBE2R1] Ubiquitin-conjugating enzyme E2 R1 (EC 2.3.2.23) ((E3-independent) E2 ubiquitin-conjugating enzyme R1) (EC 2.3.2.24) (E2 ubiquitin-conjugating enzyme R1) (Ubiquitin-conjugating enzyme E2-32 kDa complementing) (Ubiquitin-conjugating enzyme E2-CDC34) (Ubiquitin-protein ligase R1)
[UBE2D3 UBC5C UBCH5C] Ubiquitin-conjugating enzyme E2 D3 (EC 2.3.2.23) ((E3-independent) E2 ubiquitin-conjugating enzyme D3) (EC 2.3.2.24) (E2 ubiquitin-conjugating enzyme D3) (Ubiquitin carrier protein D3) (Ubiquitin-conjugating enzyme E2(17)KB 3) (Ubiquitin-conjugating enzyme E2-17 kDa 3) (Ubiquitin-protein ligase D3)
[UBE2H] Ubiquitin-conjugating enzyme E2 H (EC 2.3.2.23) ((E3-independent) E2 ubiquitin-conjugating enzyme H) (EC 2.3.2.24) (E2 ubiquitin-conjugating enzyme H) (UbcH2) (Ubiquitin carrier protein H) (Ubiquitin-conjugating enzyme E2-20K) (Ubiquitin-protein ligase H)
[UBE2W UBC16] Ubiquitin-conjugating enzyme E2 W (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme W) (N-terminal E2 ubiquitin-conjugating enzyme) (EC 2.3.2.25) (N-terminus-conjugating E2) (Ubiquitin carrier protein W) (Ubiquitin-conjugating enzyme 16) (UBC-16) (Ubiquitin-protein ligase W)
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[Cdc34 Ubch3 Ube2r1] Ubiquitin-conjugating enzyme E2 R1 (EC 2.3.2.23) ((E3-independent) E2 ubiquitin-conjugating enzyme R1) (EC 2.3.2.24) (E2 ubiquitin-conjugating enzyme R1) (Ubiquitin-conjugating enzyme E2-32 kDa complementing) (Ubiquitin-conjugating enzyme E2-CDC34) (Ubiquitin-protein ligase R1)
[UBE2K HIP2 LIG] Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme K) (Huntingtin-interacting protein 2) (HIP-2) (Ubiquitin carrier protein) (Ubiquitin-conjugating enzyme E2-25 kDa) (Ubiquitin-conjugating enzyme E2(25K)) (Ubiquitin-conjugating enzyme E2-25K) (Ubiquitin-protein ligase)
[Ube2w] Ubiquitin-conjugating enzyme E2 W (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme W) (N-terminal E2 ubiquitin-conjugating enzyme) (EC 2.3.2.25) (N-terminus-conjugating E2) (Ubiquitin carrier protein W) (Ubiquitin-protein ligase W)
[Ube2d3] Ubiquitin-conjugating enzyme E2 D3 (EC 2.3.2.23) ((E3-independent) E2 ubiquitin-conjugating enzyme D3) (EC 2.3.2.24) (E2 ubiquitin-conjugating enzyme D3) (Ubiquitin carrier protein D3) (Ubiquitin-conjugating enzyme E2(17)KB 3) (Ubiquitin-conjugating enzyme E2-17 kDa 3) (Ubiquitin-protein ligase D3)
[Ube2k Hip2] Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme K) (Huntingtin-interacting protein 2) (HIP-2) (Ubiquitin carrier protein) (Ubiquitin-conjugating enzyme E2-25 kDa) (Ubiquitin-conjugating enzyme E2(25K)) (Ubiquitin-conjugating enzyme E2-25K) (Ubiquitin-protein ligase)
[Ube2d3] Ubiquitin-conjugating enzyme E2 D3 (EC 2.3.2.23) ((E3-independent) E2 ubiquitin-conjugating enzyme D3) (EC 2.3.2.24) (E2 ubiquitin-conjugating enzyme D3) (Phosphoarginine phosphatase) (PAPase) (Ubiquitin carrier protein D3) (Ubiquitin-conjugating enzyme E2(17)KB 3) (Ubiquitin-conjugating enzyme E2-17 kDa 3) (Ubiquitin-protein ligase D3)
[SAE1A SAE1-1 At4g24940 F13M23.80] SUMO-activating enzyme subunit 1A (SUMO-activating enzyme subunit 1-1) (Ubiquitin-like 1-activating enzyme E1A)
[tat] Protein Tat (Transactivating regulatory protein)
[UBE2K HIP2] Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23) (E2 ubiquitin-conjugating enzyme K) (Huntingtin-interacting protein 2) (HIP-2) (Ubiquitin carrier protein) (Ubiquitin-conjugating enzyme E2-25 kDa) (Ubiquitin-conjugating enzyme E2(25K)) (Ubiquitin-conjugating enzyme E2-25K) (Ubiquitin-protein ligase)
[UBE2N BLU] Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) (Bendless-like ubiquitin-conjugating enzyme) (E2 ubiquitin-conjugating enzyme N) (Ubc13) (UbcH13) (Ubiquitin carrier protein N) (Ubiquitin-protein ligase N)

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