P0ADE8 (YGFZ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-modifying protein ygfZ

Gene names

Name:	ygfZ
Synonyms:	yzzW
Ordered Locus Names:	b2898, JW2866

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	326 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Folate-binding protein involved in regulating the level of ATP-dnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication. Ref.5
Subcellular location	Cytoplasm Potential HAMAP MF_01175.
Sequence similarities	Belongs to the tRNA-modifying ygfZ family.

Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Cytoplasm
Ligand	Folate-binding
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	RNA modification Inferred from genetic interaction Ref.5. Source: EcoCyc glycine catabolic process Inferred from electronic annotation. Source: InterPro tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	aminomethyltransferase activity Inferred from electronic annotation. Source: InterPro folic acid binding Inferred from direct assay Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 326

325

tRNA-modifying protein ygfZ HAMAP MF_01175

PRO_0000169834

Sites

Binding site

27

1

Folate Potential

Binding site

189

1

Folate Potential

Experimental info

Sequence conflict

8

1

P → D AA sequence Ref.3

Secondary structure

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326

Helix Strand Turn

Details...

Helix

14 – 16

3

Beta strand

19 – 23

5

Beta strand

27 – 34

8

Helix

37 – 42

6

Beta strand

45 – 47

3

Helix

49 – 51

3

Beta strand

57 – 63

7

Beta strand

69 – 78

10

Beta strand

81 – 87

7

Helix

88 – 99

12

Beta strand

103 – 106

4

Beta strand

108 – 112

5

Beta strand

114 – 122

9

Helix

125 – 130

6

Beta strand

143 – 146

4

Beta strand

149 – 154

6

Beta strand

156 – 158

3

Beta strand

160 – 165

6

Helix

167 – 177

11

Beta strand

181 – 184

4

Helix

186 – 196

11

Helix

203 – 205

3

Helix

211 – 214

4

Helix

216 – 218

3

Beta strand

224 – 226

3

Helix

232 – 237

6

Beta strand

246 – 253

8

Beta strand

265 – 269

5

Beta strand

272 – 276

5

Beta strand

278 – 284

7

Beta strand

290 – 297

8

Beta strand

306 – 308

3

Beta strand

315 – 318

4

Sequences

	Sequence		Length	Mass (Da)
	P0ADE8 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 08E050CE26B56B77	FASTA	326	36,094
	10 20 30 40 50 60 MAFTPFPPRQ PTASARLPLT LMTLDDWALA TITGADSEKY MQGQVTADVS QMAEDQHLLA 70 80 90 100 110 120 AHCDAKGKMW SNLRLFRDGD GFAWIERRSV REPQLTELKK YAVFSKVTIA PDDERVLLGV 130 140 150 160 170 180 AGFQARAALA NLFSELPSKE KQVVKEGATT LLWFEHPAER FLIVTDEATA NMLTDKLRGE 190 200 210 220 230 240 AELNNSQQWL ALNIEAGFPV IDAANSGQFI PQATNLQALG GISFKKGCYT GQEMVARAKF 250 260 270 280 290 300 RGANKRALWL LAGSASRLPE AGEDLELKMG ENWRRTGTVL AAVKLEDGQV VVQVVMNNDM 310 320 EPDSIFRVRD DANTLHIEPL PYSLEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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.
[2]	"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.
[3]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[4]	"Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography." Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B. Electrophoresis 20:2181-2195(1999) [PubMed: 10493123] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY. Strain: B / BL21.
[5]	"Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation." Ote T., Hashimoto M., Ikeuchi Y., Su'etsugu M., Suzuki T., Katayama T., Kato J. Mol. Microbiol. 59:265-275(2006) [PubMed: 16359333] [Abstract] Cited for: FUNCTION. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism." Teplyakov A., Obmolova G., Sarikaya E., Pullalarevu S., Krajewski W., Galkin A., Howard A.J., Herzberg O., Gilliland G.L. J. Bacteriol. 186:7134-7140(2004) [PubMed: 15489424] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-325, FOLATE BINDING. Strain: K12 / MG1655 / ATCC 47076.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U28375 Genomic DNA. Translation: AAA83079.1.
U00096 Genomic DNA. Translation: AAC75936.1.
AP009048 Genomic DNA. Translation: BAE76963.1.

PIR

B65074.

RefSeq

NP_417374.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NRK	X-ray	2.80	A	1-325	[»]
1VLY	X-ray	1.30	A	1-326	[»]

ProteinModelPortal

P0ADE8.

SMR

P0ADE8. Positions 1-325.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48117N.

IntAct

P0ADE8. 6 interactions.

MINT

MINT-1257340.

2D gel databases

SWISS-2DPAGE

P0ADE8.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000004601; EBESCP00000004601; EBESCG00000003750.
EBESCT00000017059; EBESCP00000016350; EBESCG00000016118.

GeneID

947384.

GenomeReviews

Gene locus JW2866 in contig AP009048_GR.
Gene locus b2898 in contig U00096_GR.

KEGG

ecj:JW2866.
eco:b2898.

PATRIC

32121210. VBIEscCol129921_2993.

Organism-specific databases

EchoBASE

EB2549.

EcoGene

EG12685. ygfZ.

Phylogenomic databases

eggNOG

COG0354.

GeneTree

EBGT00050000008933.

HOGENOM

HBG700628.

OMA

GAHCDPK.

PhylomeDB

P0ADE8.

ProtClustDB

PRK09559.

Enzyme and pathway databases

BioCyc

EcoCyc:G7511-MONOMER.

Gene expression databases

Genevestigator

P0ADE8.

Family and domain databases

HAMAP

MF_01175. tRNA-modifying_YgfZ.
[Tree]

InterPro

IPR006222. GCV_T_N.
IPR023758. tRNA-modifying_YgfZ.
IPR017703. YgfZ/GcvT_CS.
[Graphical view]

KO

K06980.

Pfam

PF01571. GCV_T. 1 hit.
[Graphical view]

TIGRFAMs

TIGR03317. YgfZ_signature. 1 hit.

ProtoNet

Search...

Entry information

Entry name

YGFZ_ECOLI

Accession

Primary (citable) accession number: P0ADE8
Secondary accession number(s): P39179, Q2M9U3, Q46826

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 6, 2005
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 58 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program