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Protein

Adenylyltransferase and sulfurtransferase UBA4

Gene

UBA4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a central role in 2-thiolation of mcm5S2U at tRNA wobble positions of cytosolic 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.6 Publications

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Pathwayi: 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis

This protein is involved in the pathway 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis, which is part of tRNA modification.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis and in tRNA modification.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei77 – 771ATP; via amide nitrogenUniRule annotation
Binding sitei98 – 981ATPUniRule annotation
Binding sitei122 – 1221ATPUniRule annotation
Metal bindingi208 – 2081ZincUniRule annotation
Metal bindingi211 – 2111ZincUniRule annotation
Active sitei225 – 2251Glycyl thioester intermediate; for adenylyltransferase activity
Metal bindingi286 – 2861ZincUniRule annotation
Metal bindingi289 – 2891ZincUniRule annotation
Active sitei397 – 3971Cysteine persulfide intermediate; for sulfurtransferase activity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi105 – 1095ATPUniRule annotation
Nucleotide bindingi166 – 1672ATPUniRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • nucleotidyltransferase activity Source: UniProtKB
  • protein adenylyltransferase activity Source: SGD
  • sulfurtransferase activity Source: UniProtKB
  • thiosulfate sulfurtransferase activity Source: SGD
  • URM1 activating enzyme activity Source: SGD

GO - Biological processi

  • cell budding Source: SGD
  • cellular response to oxidative stress Source: SGD
  • enzyme active site formation via cysteine modification to L-cysteine persulfide Source: UniProtKB
  • invasive growth in response to glucose limitation Source: SGD
  • protein urmylation Source: SGD
  • regulation of pseudohyphal growth Source: SGD
  • tRNA thio-modification Source: UniProtKB
  • tRNA wobble position uridine thiolation Source: SGD
  • tRNA wobble uridine modification Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

tRNA processing, Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31153-MONOMER.
BRENDAi2.7.7.B4. 984.
2.8.1.B2. 984.
ReactomeiR-SCE-947581. Molybdenum cofactor biosynthesis.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.
UniPathwayiUPA00988.

Names & Taxonomyi

Protein namesi
Recommended name:
Adenylyltransferase and sulfurtransferase UBA4UniRule annotation
Alternative name(s):
Needs CLA4 to survive protein 3
Ubiquitin-like protein activator 4UniRule annotation
Including the following 2 domains:
Adenylyltransferase UBA4UniRule annotation (EC:2.7.7.-UniRule annotation)
Sulfurtransferase UBA4UniRule annotation (EC:2.8.1.-UniRule annotation)
Gene namesi
Name:UBA4UniRule annotation
Synonyms:NCS3
Ordered Locus Names:YHR111W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VIII

Organism-specific databases

EuPathDBiFungiDB:YHR111W.
SGDiS000001153. UBA4.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi225 – 2251C → A or S: Abolishes adenylyltransferase activity but not sulfurtransferase activity. 4 Publications
Mutagenesisi397 – 3971C → A or S: Abolishes sulfurtransferase activity but not adenylyltransferase activity. 3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 440440Adenylyltransferase and sulfurtransferase UBA4PRO_0000120587Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources
Modified residuei326 – 3261PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP38820.

PTM databases

iPTMnetiP38820.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
URM1P405544EBI-24676,EBI-24940

Protein-protein interaction databases

BioGridi36544. 181 interactions.
DIPiDIP-1883N.
IntActiP38820. 8 interactions.
MINTiMINT-395690.

Structurei

3D structure databases

ProteinModelPortaliP38820.
SMRiP38820. Positions 43-290, 324-440.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini339 – 438100RhodaneseUniRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi214 – 2196Poly-Pro

Sequence similaritiesi

In the N-terminal section; belongs to the HesA/MoeB/ThiF family. UBA4 subfamily.UniRule annotation
Contains 1 rhodanese domain.UniRule annotation

Phylogenomic databases

GeneTreeiENSGT00810000125467.
HOGENOMiHOG000281219.
InParanoidiP38820.
KOiK11996.
OMAiGGFFKYI.
OrthoDBiEOG092C3K3Z.

Family and domain databases

Gene3Di3.40.250.10. 1 hit.
3.40.50.720. 1 hit.
HAMAPiMF_03049. MOCS3_Uba4. 1 hit.
InterProiIPR028885. MOCS3/Uba4.
IPR016040. NAD(P)-bd_dom.
IPR001763. Rhodanese-like_dom.
IPR000594. ThiF_NAD_FAD-bd.
[Graphical view]
PfamiPF00581. Rhodanese. 1 hit.
PF00899. ThiF. 1 hit.
[Graphical view]
SMARTiSM00450. RHOD. 1 hit.
[Graphical view]
SUPFAMiSSF69572. SSF69572. 1 hit.
PROSITEiPS50206. RHODANESE_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38820-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNDYHLEDTT SELEALRLEN AQLREQLAKR EDSSRDYPLS LEEYQRYGRQ
60 70 80 90 100
MIVEETGGVA GQVKLKNTKV LVVGAGGLGC PALPYLAGAG VGQIGIVDND
110 120 130 140 150
VVETSNLHRQ VLHDSSRVGM LKCESARQYI TKLNPHINVV TYPVRLNSSN
160 170 180 190 200
AFDIFKGYNY ILDCTDSPLT RYLVSDVAVN LGITVVSASG LGTEGQLTIL
210 220 230 240 250
NFNNIGPCYR CFYPTPPPPN AVTSCQEGGV IGPCIGLVGT MMAVETLKLI
260 270 280 290 300
LGIYTNENFS PFLMLYSGFP QQSLRTFKMR GRQEKCLCCG KNRTITKEAI
310 320 330 340 350
EKGEINYELF CGARNYNVCE PDERISVDAF QRIYKDDEFL AKHIFLDVRP
360 370 380 390 400
SHHYEISHFP EAVNIPIKNL RDMNGDLKKL QEKLPSVEKD SNIVILCRYG
410 420 430 440
NDSQLATRLL KDKFGFSNVR DVRGGYFKYI DDIDQTIPKY
Length:440
Mass (Da):49,361
Last modified:February 1, 1995 - v1
Checksum:iCF686FCA74D29F30
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00059 Genomic DNA. Translation: AAB68852.1.
BK006934 Genomic DNA. Translation: DAA06805.1.
PIRiS48953.
RefSeqiNP_011979.1. NM_001179241.1.

Genome annotation databases

EnsemblFungiiYHR111W; YHR111W; YHR111W.
GeneIDi856511.
KEGGisce:YHR111W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00059 Genomic DNA. Translation: AAB68852.1.
BK006934 Genomic DNA. Translation: DAA06805.1.
PIRiS48953.
RefSeqiNP_011979.1. NM_001179241.1.

3D structure databases

ProteinModelPortaliP38820.
SMRiP38820. Positions 43-290, 324-440.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36544. 181 interactions.
DIPiDIP-1883N.
IntActiP38820. 8 interactions.
MINTiMINT-395690.

PTM databases

iPTMnetiP38820.

Proteomic databases

MaxQBiP38820.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYHR111W; YHR111W; YHR111W.
GeneIDi856511.
KEGGisce:YHR111W.

Organism-specific databases

EuPathDBiFungiDB:YHR111W.
SGDiS000001153. UBA4.

Phylogenomic databases

GeneTreeiENSGT00810000125467.
HOGENOMiHOG000281219.
InParanoidiP38820.
KOiK11996.
OMAiGGFFKYI.
OrthoDBiEOG092C3K3Z.

Enzyme and pathway databases

UniPathwayiUPA00988.
BioCyciYEAST:G3O-31153-MONOMER.
BRENDAi2.7.7.B4. 984.
2.8.1.B2. 984.
ReactomeiR-SCE-947581. Molybdenum cofactor biosynthesis.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

PROiP38820.

Family and domain databases

Gene3Di3.40.250.10. 1 hit.
3.40.50.720. 1 hit.
HAMAPiMF_03049. MOCS3_Uba4. 1 hit.
InterProiIPR028885. MOCS3/Uba4.
IPR016040. NAD(P)-bd_dom.
IPR001763. Rhodanese-like_dom.
IPR000594. ThiF_NAD_FAD-bd.
[Graphical view]
PfamiPF00581. Rhodanese. 1 hit.
PF00899. ThiF. 1 hit.
[Graphical view]
SMARTiSM00450. RHOD. 1 hit.
[Graphical view]
SUPFAMiSSF69572. SSF69572. 1 hit.
PROSITEiPS50206. RHODANESE_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUBA4_YEAST
AccessioniPrimary (citable) accession number: P38820
Secondary accession number(s): D3DL61
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 7, 2016
This is version 147 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2620 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.