P77806 (YBDL_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Aminotransferase YbdL
EC=2.6.1.-

Gene names

Name:	ybdL
Ordered Locus Names:	b0600, JW0593

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	386 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Shows aminotransferase activity with methionine and histidine as substrates, and to a lesser extent also with phenylalanine. Ref.5
Cofactor	Pyridoxal phosphate.
Subunit structure	Homodimer. Ref.5
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Aminotransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	biosynthetic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	methionine-oxo-acid transaminase activity Inferred from direct assay Ref.5. Source: EcoCyc pyridoxal phosphate binding Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 386

386

Aminotransferase YbdL

PRO_0000123925

Amino acid modifications

Modified residue

236

1

N6-(pyridoxal phosphate)lysine

Secondary structure

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386

Helix Strand Turn

Details...

Helix

19 – 29

11

Helix

46 – 57

12

Helix

70 – 84

15

Turn

90 – 93

4

Beta strand

94 – 99

6

Helix

100 – 111

12

Beta strand

117 – 123

7

Helix

128 – 134

7

Beta strand

138 – 143

6

Turn

146 – 148

3

Helix

153 – 159

7

Beta strand

164 – 172

9

Turn

174 – 176

3

Helix

182 – 192

11

Beta strand

198 – 202

5

Turn

204 – 207

4

Helix

218 – 220

3

Helix

222 – 225

4

Beta strand

228 – 233

6

Helix

234 – 237

4

Helix

241 – 243

3

Beta strand

246 – 249

4

Helix

252 – 265

14

Helix

271 – 283

13

Helix

286 – 289

4

Helix

291 – 305

15

Beta strand

308 – 310

3

Beta strand

318 – 325

8

Turn

327 – 329

3

Helix

334 – 344

11

Helix

352 – 355

4

Beta strand

364 – 368

5

Helix

373 – 383

11

Sequences

	Sequence		Length	Mass (Da)
	P77806 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: A95A782EA910B13F	FASTA	386	42,963
	10 20 30 40 50 60 MTNNPLIPQS KLPQLGTTIF TQMSALAQQH QAINLSQGFP DFDGPRYLQE RLAHHVAQGA 70 80 90 100 110 120 NQYAPMTGVQ ALREAIAQKT ERLYGYQPDA DSDITVTAGA TEALYAAITA LVRNGDEVIC 130 140 150 160 170 180 FDPSYDSYAP AIALSGGIVK RMALQPPHFR VDWQEFAALL SERTRLVILN TPHNPSATVW 190 200 210 220 230 240 QQADFAALWQ AIAGHEIFVI SDEVYEHINF SQQGHASVLA HPQLRERAVA VSSFGKTYHM 250 260 270 280 290 300 TGWKVGYCVA PAPISAEIRK VHQYLTFSVN TPAQLALADM LRAEPEHYLA LPDFYRQKRD 310 320 330 340 350 360 ILVNALNESR LEILPCEGTY FLLVDYSAVS TLDDVEFCQW LTQEHGVAAI PLSVFCADPF 370 380 PHKLIRLCFA KKESTLLAAA ERLRQL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function." Dolzan M., Johansson K., Roig-Zamboni V., Campanacci V., Tegoni M., Schneider G., Cambillau C. FEBS Lett. 571:141-146(2004) [PubMed: 15280032] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE, FUNCTION, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-236.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U82598 Genomic DNA. Translation: AAB40801.1.
U00096 Genomic DNA. Translation: AAC73701.1.
AP009048 Genomic DNA. Translation: BAA35230.1.

PIR

F64793.

RefSeq

NP_415133.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U08	X-ray	2.35	A/B	1-386	[»]

ProteinModelPortal

P77806.

SMR

P77806. Positions 5-386.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11350N.

IntAct

P77806. 7 interactions.

MINT

MINT-1306557.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001787; EBESCP00000001787; EBESCG00000001472.
EBESCT00000015001; EBESCP00000014292; EBESCG00000014061.

GeneID

945211.

GenomeReviews

Gene locus JW0593 in contig AP009048_GR.
Gene locus b0600 in contig U00096_GR.

KEGG

ecj:JW0593.
eco:b0600.

PATRIC

32116378. VBIEscCol129921_0629.

Organism-specific databases

EchoBASE

EB3302.

EcoGene

EG13531. ybdL.

Phylogenomic databases

eggNOG

COG0436.

GeneTree

EBGT00050000008899.

HOGENOM

HBG645860.

OMA

YSPAIAL.

PhylomeDB

P77806.

ProtClustDB

PRK09082.

Enzyme and pathway databases

BioCyc

EcoCyc:G6329-MONOMER.
MetaCyc:G6329-MONOMER.

Gene expression databases

Genevestigator

P77806.

Family and domain databases

InterPro

IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase_major_dom.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]

Gene3D

G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.
G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.

KO

K14287.

Pfam

PF00155. Aminotran_1_2. 1 hit.
[Graphical view]

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

PROSITE

PS00105. AA_TRANSFER_CLASS_1. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

YBDL_ECOLI

Accession

Primary (citable) accession number: P77806

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	February 1, 1997
Last modified:	January 25, 2012
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program