P38820 (UBA4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Adenylyltransferase and sulfurtransferase UBA4

Alternative name(s):
Needs CLA4 to survive protein 3
Ubiquitin-like protein activator 4

Including the following 2 domains:

1. Adenylyltransferase UBA4
   EC=2.7.7.-
2. Sulfurtransferase UBA4
   EC=2.8.1.-

Gene names

Name:	UBA4
Synonyms:	NCS3
Ordered Locus Names:	YHR111W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	440 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Plays a central role in 2-thiolation of mcm5S2U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Acts by mediating the C-terminal thiocarboxylation of sulfur carrier URM1. Its N-terminus first activates URM1 as acyl-adenylates (-COAMP), then the persulfide sulfur on the catalytic cysteine is transferred to URM1 to form thiocarboxylation (-COSH) of its C-terminus. The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards URM1. Subsequently, a transient disulfide bond is formed. Does not use thiosulfate as sulfur donor; NFS1 probably acting as a sulfur donor for thiocarboxylation reactions. Prior mcm5 tRNA modification by the elongator complex is required for 2-thiolation. May also be involved in protein urmylation. Ref.3 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11
Cofactor	Binds 1 zinc ion per subunit By similarity.
Pathway	tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis.
Subcellular location	Cytoplasm Ref.4.
Miscellaneous	Present with 2620 molecules/cell in log phase SD medium.
Sequence similarities	In the N-terminal section; belongs to the HesA/MoeB/ThiF family. UBA4 subfamily. Contains 1 rhodanese domain.

Ontologies

Keywords
Biological process	Ubl conjugation pathway tRNA processing
Cellular component	Cytoplasm
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	cell budding Inferred from genetic interaction PubMed 14551258. Source: SGD cellular response to oxidative stress Inferred from mutant phenotype PubMed 14555475. Source: SGD enzyme active site formation via L-cysteine persulfide Inferred from mutant phenotype Ref.11. Source: UniProtKB invasive growth in response to glucose limitation Inferred from mutant phenotype PubMed 14551258. Source: SGD protein urmylation Inferred from direct assay Ref.3. Source: SGD regulation of pseudohyphal growth Inferred from mutant phenotype PubMed 22043304. Source: SGD tRNA wobble position uridine thiolation Inferred from mutant phenotype Ref.8Ref.10Ref.11. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay Ref.4. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW URM1 activating enzyme activity Inferred from direct assay Ref.3. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein adenylyltransferase activity Inferred from mutant phenotype Ref.10. Source: SGD thiosulfate sulfurtransferase activity Inferred from direct assay PubMed 19864628. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
URM1	P40554	4	EBI-24676,EBI-24940

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 440	440	Adenylyltransferase and sulfurtransferase UBA4		PRO_0000120587
Regions
	Domain	339 – 438	100	Rhodanese
	Nucleotide binding	105 – 109	5	ATP By similarity
	Nucleotide binding	166 – 167	2	ATP By similarity
	Compositional bias	214 – 219	6	Poly-Pro
Sites
	Active site	225	1	Glycyl thioester intermediate; for adenylyltransferase activity
	Active site	397	1	Cysteine persulfide intermediate; for sulfurtransferase activity
	Metal binding	208	1	Zinc By similarity
	Metal binding	211	1	Zinc By similarity
	Metal binding	286	1	Zinc By similarity
	Metal binding	289	1	Zinc By similarity
	Binding site	77	1	ATP; via amide nitrogen By similarity
	Binding site	98	1	ATP By similarity
	Binding site	122	1	ATP By similarity
Amino acid modifications
	Modified residue	326	1	Phosphoserine Ref.6
Experimental info
	Mutagenesis	225	1	C → A or S: Abolishes adenylyltransferase activity but not sulfurtransferase activity. Ref.3 Ref.7 Ref.10 Ref.11
	Mutagenesis	397	1	C → A or S: Abolishes sulfurtransferase activity but not adenylyltransferase activity. Ref.7 Ref.10 Ref.11

Sequences

	Sequence		Length	Mass (Da)
	P38820 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: CF686FCA74D29F30	FASTA	440	49,361
	10 20 30 40 50 60 MNDYHLEDTT SELEALRLEN AQLREQLAKR EDSSRDYPLS LEEYQRYGRQ MIVEETGGVA 70 80 90 100 110 120 GQVKLKNTKV LVVGAGGLGC PALPYLAGAG VGQIGIVDND VVETSNLHRQ VLHDSSRVGM 130 140 150 160 170 180 LKCESARQYI TKLNPHINVV TYPVRLNSSN AFDIFKGYNY ILDCTDSPLT RYLVSDVAVN 190 200 210 220 230 240 LGITVVSASG LGTEGQLTIL NFNNIGPCYR CFYPTPPPPN AVTSCQEGGV IGPCIGLVGT 250 260 270 280 290 300 MMAVETLKLI LGIYTNENFS PFLMLYSGFP QQSLRTFKMR GRQEKCLCCG KNRTITKEAI 310 320 330 340 350 360 EKGEINYELF CGARNYNVCE PDERISVDAF QRIYKDDEFL AKHIFLDVRP SHHYEISHFP 370 380 390 400 410 420 EAVNIPIKNL RDMNGDLKKL QEKLPSVEKD SNIVILCRYG NDSQLATRLL KDKFGFSNVR 430 440 DVRGGYFKYI DDIDQTIPKY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"A protein conjugation system in yeast with homology to biosynthetic enzyme reaction of prokaryotes." Furukawa K., Mizushima N., Noda T., Ohsumi Y. J. Biol. Chem. 275:7462-7465(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH URM1, MUTAGENESIS OF CYS-225.
[4]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[5]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-326, MASS SPECTROMETRY.
[7]	"The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins." Schmitz J., Chowdhury M.M., Haenzelmann P., Nimtz M., Lee E.Y., Schindelin H., Leimkuehler S. Biochemistry 47:6479-6489(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN 2-THIOLATION OF TRNA, MUTAGENESIS OF CYS-225 AND CYS-397.
[8]	"Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems." Nakai Y., Nakai M., Hayashi H. J. Biol. Chem. 283:27469-27476(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN 2-THIOLATION OF TRNA.
[9]	"A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae." Huang B., Lu J., Bystroem A.S. RNA 14:2183-2194(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN 2-THIOLATION OF TRNA.
[10]	"Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA." Leidel S., Pedrioli P.G.A., Bucher T., Brost R., Costanzo M., Schmidt A., Aebersold R., Boone C., Hofmann K., Peter M. Nature 458:228-233(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN 2-THIOLATION OF TRNA, INTERACTION WITH NCS2; NCS6 AND URM1, MUTAGENESIS OF CYS-225 AND CYS-397.
[11]	"Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions." Noma A., Sakaguchi Y., Suzuki T. Nucleic Acids Res. 37:1335-1352(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN 2-THIOLATION OF TRNA, INTERACTION WITH URM1, MUTAGENESIS OF CYS-225 AND CYS-397.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00059 Genomic DNA. Translation: AAB68852.1. BK006934 Genomic DNA. Translation: DAA06805.1.
PIR	S48953.
RefSeq	NP_011979.1. NM_001179241.1.
3D structure databases
ProteinModelPortal	P38820.
SMR	P38820. Positions 43-290, 324-440.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1883N.
IntAct	P38820. 8 interactions.
MINT	MINT-395690.
STRING	4932.YHR111W.
Proteomic databases
PaxDb	P38820.
PeptideAtlas	P38820.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YHR111W; YHR111W; YHR111W.
GeneID	856511.
KEGG	sce:YHR111W.
Organism-specific databases
CYGD	YHR111w.
SGD	S000001153. UBA4.
Phylogenomic databases
eggNOG	COG0476.
GeneTree	ENSGT00570000079161.
HOGENOM	HOG000281219.
KO	K11996.
OMA	LCRYGND.
OrthoDB	EOG48KVM4.
Enzyme and pathway databases
BioCyc	YEAST:G3O-31153-MONOMER.
UniPathway	UPA00988.
Gene expression databases
Genevestigator	P38820.
GermOnline	YHR111W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.40.250.10. 1 hit. 3.40.50.720. 1 hit.
InterPro	IPR007901. MoeZ_MoeB. IPR009036. Molybdenum_cofac_synth_MoeB. IPR016040. NAD(P)-bd_dom. IPR001763. Rhodanese-like_dom. IPR000594. ThiF_NAD_FAD-bd. [Graphical view]
Pfam	PF05237. MoeZ_MoeB. 1 hit. PF00581. Rhodanese. 1 hit. PF00899. ThiF. 1 hit. [Graphical view]
SMART	SM00450. RHOD. 1 hit. [Graphical view]
SUPFAM	SSF69572. MoeB. 1 hit.
PROSITE	PS50206. RHODANESE_3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	982251.

Entry information

Entry name

UBA4_YEAST

Accession

Primary (citable) accession number: P38820
Secondary accession number(s): D3DL61

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 118 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program