P38197 (YBD6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
UPF0001 protein YBL036C

Gene names

Ordered Locus Names:	YBL036C
ORF Names:	YBL0413

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	257 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Cofactor	Pyridoxal phosphate. Ref.6
Miscellaneous	Present with 4890 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the UPF0001 family.

Ontologies

Keywords
Ligand	Pyridoxal phosphate
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Molecular function	pyridoxal phosphate binding Inferred from direct assay Ref.6. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-21226,EBI-21226

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 257

257

UPF0001 protein YBL036C

PRO_0000163213

Amino acid modifications

Modified residue

49

1

N6-(pyridoxal phosphate)lysine

Experimental info

Sequence conflict

8

1

D → G in AAT92893. Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

257

Helix Strand Turn

Details...

Helix

9 – 30

22

Beta strand

43 – 47

5

Helix

53 – 62

10

Beta strand

66 – 69

4

Helix

72 – 81

10

Beta strand

87 – 90

4

Helix

96 – 98

3

Helix

99 – 103

5

Beta strand

108 – 114

7

Helix

117 – 130

14

Beta strand

132 – 134

3

Beta strand

137 – 143

7

Beta strand

146 – 148

3

Beta strand

151 – 154

4

Helix

157 – 167

11

Beta strand

174 – 181

8

Helix

197 – 213

17

Beta strand

218 – 220

3

Turn

224 – 226

3

Helix

227 – 232

6

Beta strand

236 – 240

5

Helix

242 – 245

4

Sequences

	Sequence		Length	Mass (Da)
	P38197 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: 5643EE0D36B6D85A	FASTA	257	29,123
	10 20 30 40 50 60 MSTGITYDED RKTQLIAQYE SVREVVNAEA KNVHVNENAS KILLLVVSKL KPASDIQILY 70 80 90 100 110 120 DHGVREFGEN YVQELIEKAK LLPDDIKWHF IGGLQTNKCK DLAKVPNLYS VETIDSLKKA 130 140 150 160 170 180 KKLNESRAKF QPDCNPILCN VQINTSHEDQ KSGLNNEAEI FEVIDFFLSE ECKYIKLNGL 190 200 210 220 230 240 MTIGSWNVSH EDSKENRDFA TLVEWKKKID AKFGTSLKLS MGMSADFREA IRQGTAEVRI 250 GTDIFGARPP KNEARII

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The sequence of a 22.4 kb DNA fragment from the left arm of yeast chromosome II reveals homologues to bacterial proline synthetase and murine alpha-adaptin, as well as a new permease and a DNA-binding protein." de Wergifosse P., Jacques B., Jonniaux J.-L., Purnelle B., Skala J., Goffeau A. Yeast 10:1489-1496(1994) [PubMed: 7871888] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed: 7813418] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"Structure of a yeast hypothetical protein selected by a structural genomics approach." Eswaramoorthy S., Gerchman S., Graziano V., Kycia H., Studier W., Swaminathan S. Acta Crystallogr. D 59:127-135(2003) [PubMed: 12499548] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH COFACTOR, PYRIDOXAL PHOSPHATE AT LYS-49. Strain: ATCC 204508 / S288c.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X78214 Genomic DNA. Translation: CAA55058.1.
Z35797 Genomic DNA. Translation: CAA84856.1.
AY692874 Genomic DNA. Translation: AAT92893.1.
BK006936 Genomic DNA. Translation: DAA07083.1.

PIR

S50294.

RefSeq

NP_009517.1. NM_001178276.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B54	X-ray	2.10	A	1-257	[»]
1CT5	X-ray	2.00	A	2-257	[»]

ProteinModelPortal

P38197.

SMR

P38197. Positions 4-246.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6608N.

IntAct

P38197. 12 interactions.

MINT

MINT-624974.

STRING

P38197.

Proteomic databases

PeptideAtlas

P38197.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBL036C; YBL036C; YBL036C.

GeneID

852244.

KEGG

sce:YBL036C.

NMPDR

fig|4932.3.peg.209.

Organism-specific databases

CYGD

YBL036c.

SGD

S000000132. YBL036C.

Phylogenomic databases

eggNOG

fuNOG07990.

GeneTree

EFGT00050000005901.

HOGENOM

HBG289671.

OMA

ECSMGMS.

OrthoDB

EOG4QRMDH.

Gene expression databases

ArrayExpress

P38197.

Genevestigator

P38197.

GermOnline

YBL036C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001608. Ala_racemase_N.
IPR011078. UPF0001.
[Graphical view]

KO

K06997.

PANTHER

PTHR10146. PP_YBL036C. 1 hit.

Pfam

PF01168. Ala_racemase_N. 1 hit.
[Graphical view]

PIRSF

PIRSF004848. YBL036c_PLPDEIII. 1 hit.

TIGRFAMs

TIGR00044. TIGR00044. 1 hit.

PROSITE

PS01211. UPF0001. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

970802.

Entry information

Entry name

YBD6_YEAST

Accession

Primary (citable) accession number: P38197
Secondary accession number(s): D6VPW3, Q6B256

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	December 14, 2011
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program