P34209 (YDCF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein ydcF

Gene names

Name:	ydcF
Ordered Locus Names:	b1414, JW1411

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	266 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Binds S-adenosyl-L-methionine (AdoMet).
Subunit structure	Monomer. Ref.6
Sequence similarities	To S.coelicolor SCO4629.
Sequence caution	The sequence AAA24246.1 differs from that shown. Reason: Frameshift at positions 8 and 23.

Ontologies

Keywords
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
None. [Check GOA]

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 266

266

Protein ydcF

PRO_0000168929

Experimental info

Sequence conflict

97

1

A → R in AAA24246. Ref.1

Sequence conflict

217 – 266

50

PRLRD…SRSLR → RVYAMIAMATVPAGEILSFT LIFRQKSSMHGKR Ref.1

Secondary structure

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266

Helix Strand Turn

Details...

Helix

11 – 25

15

Turn

29 – 32

4

Beta strand

38 – 44

7

Helix

48 – 61

14

Beta strand

65 – 68

4

Helix

75 – 83

9

Helix

88 – 90

3

Helix

98 – 108

11

Helix

114 – 116

3

Beta strand

117 – 120

4

Helix

126 – 138

13

Beta strand

147 – 150

4

Turn

153 – 155

3

Helix

156 – 167

12

Beta strand

175 – 178

4

Beta strand

186 – 189

4

Beta strand

192 – 197

6

Helix

205 – 219

15

Beta strand

225 – 227

3

Turn

228 – 231

4

Helix

241 – 251

11

Helix

254 – 262

9

Sequences

	Sequence		Length	Mass (Da)
	P34209 [UniParc]. Last modified November 1, 1997. Version 3. Checksum: DA59CFB3D34728A5	FASTA	266	29,706
	10 20 30 40 50 60 MNITPFPTLS PATIDAINVI GQWLAQDDFS GEVPYQADCV ILAGNAVMPT IDAACKIARD 70 80 90 100 110 120 QQIPLLISGG IGHSTTFLYS AIAQHPHYNT IRTTGRAEAT ILADIAHQFW HIPHEKIWIE 130 140 150 160 170 180 DQSTNCGENA RFSIALLNQA VERVHTAIVV QDPTMQRRTM ATFRRMTGDN PDAPRWLSYP 190 200 210 220 230 240 GFVPQLGNNA DSVIFINQLQ GLWPVERYLS LLTGELPRLR DDSDGYGPRG RDFIVHVDFP 250 260 AEVIHAWQTL KHDAVLIEAM ESRSLR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A third gene with high homology to gap gene in the Escherichia coli chromosome." Hidalgo E., Limon A., Aguilar J. Submitted (NOV-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed: 9097039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[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]	"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.
[6]	"The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes." Chao K.L., Lim K., Lehmann C., Doseeva V., Howard A.J., Schwarz F.P., Herzberg O. Proteins 72:506-509(2008) [PubMed: 18393394] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SUBUNIT, S-ADENOSYL-L-METHIONINE BINDING.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L09068 Genomic DNA. Translation: AAA24246.1. Frameshift.
U00096 Genomic DNA. Translation: AAC74496.1.
AP009048 Genomic DNA. Translation: BAA15030.1.

PIR

A64893.

RefSeq

NP_415932.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3CA8	X-ray	1.80	A/B	1-266	[»]

ProteinModelPortal

P34209.

SMR

P34209. Positions 5-265.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11642N.

IntAct

P34209. 1 interaction.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001921; EBESCP00000001921; EBESCG00000001575.
EBESCT00000016382; EBESCP00000015673; EBESCG00000015442.

GeneID

946215.

GenomeReviews

Gene locus JW1411 in contig AP009048_GR.
Gene locus b1414 in contig U00096_GR.

KEGG

ecj:JW1411.
eco:b1414.

PATRIC

32118114. VBIEscCol129921_1477.

Organism-specific databases

EchoBASE

EB2033.

EcoGene

EG12110. ydcF.

Phylogenomic databases

eggNOG

COG1434.

GeneTree

EBGT00050000009273.

HOGENOM

HBG325510.

OMA

TNCGNNI.

ProtClustDB

CLSK880080.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12110-MONOMER.

Gene expression databases

Genevestigator

P34209.

Family and domain databases

InterPro

IPR003848. DUF218.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]

Gene3D

G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.

Pfam

PF02698. DUF218. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

YDCF_ECOLI

Accession

Primary (citable) accession number: P34209
Secondary accession number(s): P77578

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	November 1, 1997
Last modified:	January 25, 2012
This is version 79 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program