P45202 (YBAK_HAEIN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase ybaK

Gene names

Name:	ybaK
Ordered Locus Names:	HI_1434

Organism

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Taxonomic identifier

71421 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pasteurellales › Pasteurellaceae › Haemophilus

Protein attributes

Sequence length	158 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Functions in trans to edit the amino acid from incorrectly charged Cys-tRNA(Pro); has much weaker activity against Ala-tRNA(Pro). Probably compensates for the lack of Cys-tRNA(Pro) editing by ProRS. Additionally serves as a general deacylase with weak activity against Cys-tRNA(Cys) and Gly-tRNA(Gly), as well as, at higher concentrations, some other correctly charged tRNAs.
Subunit structure	May form a tertiary complex with ProRS and t-RNA(Pro), as it can be cross-linked to E.coli ProRS and to E.coli tRNA(Pro) in vitro. It cannot compete with Ef-Tu for aminoacyl-tRNA binding, suggesting it acts before release of the charged aminoacyl-tRNA from the synthetase. Ref.5
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the prolyl-tRNA editing family. ProX subfamily.

Ontologies

Keywords
Cellular component	Cytoplasm
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	Ala-tRNA(Pro) hydrolase activity Inferred from direct assay Ref.3. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 158

158

Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase ybaK

PRO_0000168623

Experimental info

Mutagenesis

46

1

K → A: Complete loss of deacylation. Ref.3

Sequence conflict

117

1

N → K in AAC23081. Ref.1

Secondary structure

1

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158

Helix Strand Turn

Details...

Helix

3 – 11

9

Beta strand

16 – 19

4

Helix

32 – 37

6

Helix

41 – 43

3

Beta strand

44 – 52

9

Beta strand

58 – 65

8

Helix

72 – 78

7

Beta strand

84 – 86

3

Helix

89 – 96

8

Beta strand

105 – 107

3

Beta strand

114 – 117

4

Helix

118 – 122

5

Beta strand

126 – 129

4

Beta strand

135 – 139

5

Helix

141 – 148

8

Beta strand

151 – 153

3

Sequences

	Sequence		Length	Mass (Da)
	P45202 [UniParc]. Last modified February 21, 2001. Version 2. Checksum: 45723E9DFC99535A	FASTA	158	17,155
	10 20 30 40 50 60 MTPAIDLLKK QKIPFILHTY DHDPNNQHFG DEAAEKLGID PNRSFKTLLV AENGDQKKLA 70 80 90 100 110 120 CFVLATANML NLKKAAKSIG VKKVEMADKD AAQKSTGYLV GGISPLGQKK RVKTVINSTA 130 140 150 LEFETIYVSG GKRGLSVEIA PQDLAKVLGA EFTDIVDE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd." Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M., McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D., Scott J.D., Shirley R., Liu L.-I. , Glodek A., Kelley J.M., Weidman J.F., Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R., Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D., Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A., Small K.V., Fraser C.M., Smith H.O., Venter J.C. Science 269:496-512(1995) [PubMed: 7542800] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.
[2]	Bonander N., Eisenstein E. Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.
[3]	"An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing." Wong F.-C., Beuning P.J., Silvers C., Musier-Forsyth K. J. Biol. Chem. 278:52857-52864(2003) [PubMed: 14530268] [Abstract] Cited for: CHARACTERIZATION OF TRNA EDITING ACTIVITY ON ALA-TRNA(PRO), MUTAGENESIS OF LYS-46.
[4]	"The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase." Ruan B., Soll D. J. Biol. Chem. 280:25887-25891(2005) [PubMed: 15886196] [Abstract] Cited for: CHARACTERIZATION OF GENERAL DEACYLASE ACTIVITY.
[5]	"Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex." An S., Musier-Forsyth K. J. Biol. Chem. 280:34465-34472(2005) [PubMed: 16087664] [Abstract] Cited for: SUBUNIT.
[6]	"Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8-A resolution: functional implications." Zhang H., Huang K., Li Z., Banerjei L., Fisher K.E., Grishin N.V., Eisenstein E., Herzberg O. Proteins 40:86-97(2000) [PubMed: 10813833] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L42023 Genomic DNA. Translation: AAC23081.1.
AF174386 Genomic DNA. Translation: AAD54290.1.

PIR

H64171.

RefSeq

NP_439583.1. NC_000907.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DBU	X-ray	1.80	A	1-158	[»]
1DBX	X-ray	1.80	A/B	1-158	[»]

ProteinModelPortal

P45202.

SMR

P45202. Positions 2-158.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

949657.

GenomeReviews

Gene locus HI_1434 in contig L42023_GR.

KEGG

hin:HI1434.

PATRIC

20191563. VBIHaeInf48452_1491.

TIGR

HI_1434.

Phylogenomic databases

HOGENOM

HBG727700.

OMA

VSPLGQK.

ProtClustDB

CLSK870129.

Enzyme and pathway databases

BioCyc

HINF71421:HI_1434-MONOMER.

Family and domain databases

InterPro

IPR004369. Prolyl-tRNA_editing_YbaK/EbsC.
IPR007214. YbaK/aa-tRNA-synth-assoc-dom.
[Graphical view]

Gene3D

G3DSA:3.90.960.10. YbaK/aa-tRNA-synth-assoc-reg. 1 hit.

Pfam

PF04073. YbaK. 1 hit.
[Graphical view]

SUPFAM

SSF55826. YbaK/aa-tRNA-synth-assoc-reg. 1 hit.

TIGRFAMs

TIGR00011. YbaK_EbsC. 1 hit.

ProtoNet

Search...

Entry information

Entry name

YBAK_HAEIN

Accession

Primary (citable) accession number: P45202
Secondary accession number(s): Q9RP30

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	February 21, 2001
Last modified:	January 25, 2012
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program