P0A6D5 (YDIB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Quinate/shikimate dehydrogenase
EC=1.1.1.282

Alternative name(s):
NAD-dependent shikimate 5-dehydrogenase 2

Gene names

Name:	ydiB
Ordered Locus Names:	b1692, JW1682

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	288 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The physiological substrate is not known. Ref.7
Catalytic activity	L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H. Ref.8 Shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H. Ref.8
Pathway	Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. HAMAP MF_01578
Subunit structure	Homodimer. Ref.7 Ref.8
Induction	Induced under carbon limitation but not under phosphate limitation. Ref.6
Sequence similarities	Belongs to the shikimate dehydrogenase family.
Sequence caution	The sequence CAA27848.1 differs from that shown. Reason: Frameshift at positions 170, 200 and 212.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Aromatic amino acid biosynthesis
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	aromatic amino acid family biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	nucleotide binding Inferred from electronic annotation. Source: InterPro quinate 3-dehydrogenase (NAD+) activity Inferred from electronic annotation. Source: EC quinate 3-dehydrogenase (NADP+) activity Inferred from electronic annotation. Source: EC shikimate 3-dehydrogenase (NAD+) activity Inferred from electronic annotation. Source: EC shikimate 3-dehydrogenase (NADP+) activity Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
hemE	P29680	1	EBI-560638,EBI-1125078
yggG	P25894	1	EBI-560638,EBI-560654

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 288

288

Quinate/shikimate dehydrogenase HAMAP MF_01578

PRO_0000136069

Regions

Nucleotide binding

131 – 135

5

NAD HAMAP MF_01578

Nucleotide binding

155 – 158

4

NAD HAMAP MF_01578

Nucleotide binding

255 – 259

5

NAD HAMAP MF_01578

Sites

Active site

71

1

Proton acceptor Potential

Binding site

107

1

Substrate Probable

Binding site

205

1

NAD; via amide nitrogen

Binding site

235

1

NAD

Experimental info

Mutagenesis

67

1

S → A: Reduces activity towards quinate about 6-fold. Ref.5

Mutagenesis

71

1

K → A: Increases KM for quinate 3200-fold. Increases KM for shikimate 170-fold. Ref.5

Mutagenesis

92

1

N → A: Alters protein structure. Loss of activity. Ref.5

Mutagenesis

106

1

T → A: Increases KM for quinate 2000-fold. Increases KM for shikimate 70-fold. Ref.5

Mutagenesis

107

1

D → A: Loss of activity towards quinate. Increases KM for shikimate 20000-fold. Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

288

Helix Strand Turn

Details...

Beta strand

8 – 16

9

Helix

22 – 32

11

Beta strand

36 – 43

8

Turn

46 – 48

3

Helix

49 – 58

10

Beta strand

62 – 66

5

Helix

73 – 77

5

Beta strand

79 – 81

3

Helix

83 – 88

6

Beta strand

92 – 97

6

Beta strand

100 – 104

5

Helix

106 – 117

12

Beta strand

126 – 130

5

Helix

134 – 145

12

Beta strand

149 – 155

7

Helix

159 – 174

16

Beta strand

178 – 183

6

Turn

187 – 190

4

Helix

191 – 194

4

Beta strand

198 – 202

5

Helix

220 – 222

3

Beta strand

228 – 231

4

Beta strand

235 – 238

4

Helix

240 – 245

6

Turn

246 – 249

4

Helix

255 – 271

17

Helix

277 – 283

7

Sequences

	Sequence		Length	Mass (Da)
	P0A6D5 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: C3D1415E03820A5A	FASTA	288	31,228
	10 20 30 40 50 60 MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPFTYM AFEVDNDSFP GAIEGLKALK 70 80 90 100 110 120 MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY LRGYNTDGTG HIRAIKESGF 130 140 150 160 170 180 DIKGKTMVLL GAGGASTAIG AQGAIEGLKE IKLFNRRDEF FDKALAFAQR VNENTDCVVT 190 200 210 220 230 240 VTDLADQQAF AEALASADIL TNGTKVGMKP LENESLVNDI SLLHPGLLVT ECVYNPHMTK 250 260 270 280 LLQQAQQAGC KTIDGYGMLL WQGAEQFTLW TGKDFPLEYV KQVMGFGA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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.
[2]	"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.
[3]	"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.
[4]	"The overexpression and complete amino acid sequence of Escherichia coli 3-dehydroquinase." Duncan K., Chaudhuri S., Campbell M.S., Coggins J.R. Biochem. J. 238:475-483(1986) [PubMed: 3541912] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 67-288. Strain: K12.
[5]	"Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli." Lindner H.A., Nadeau G., Matte A., Michel G., Menard R., Cygler M. J. Biol. Chem. 280:7162-7169(2005) [PubMed: 15596430] [Abstract] Cited for: MUTAGENESIS OF SER-67; LYS-71; ASN-92; THR-106 AND ASP-107, MASS SPECTROMETRY.
[6]	"Transcriptome analysis of a shikimic acid producing strain of Escherichia coli W3110 grown under carbon- and phosphate-limited conditions." Johansson L., Liden G. J. Biotechnol. 126:528-545(2006) [PubMed: 16828913] [Abstract] Cited for: INDUCTION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase." Benach J., Lee I., Edstrom W., Kuzin A.P., Chiang Y., Acton T.B., Montelione G.T., Hunt J.F. J. Biol. Chem. 278:19176-19182(2003) [PubMed: 12624088] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION, SUBUNIT.
[8]	"Structures of shikimate dehydrogenase AroE and its paralog YdiB. A common structural framework for different activities." Michel G., Roszak A.W., Sauve V., Maclean J., Matte A., Coggins J.R., Cygler M., Lapthorn A.J. J. Biol. Chem. 278:19463-19472(2003) [PubMed: 12637497] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NAD, CATALYTIC ACTIVITY, SUBUNIT.
[9]	"Structural analysis of a set of proteins resulting from a bacterial genomics project." Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G., Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S., Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D., Hendle J. , Huber A., Hoda K., Kearins P., Kissinger C., Laubert B., Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M., Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M., Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S., Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J., Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R. Proteins 60:787-796(2005) [PubMed: 16021622] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-288 IN COMPLEX WITH NAD.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00096 Genomic DNA. Translation: AAC74762.1.
AP009048 Genomic DNA. Translation: BAA15449.1.
X04306 Genomic DNA. Translation: CAA27848.1. Frameshift.

PIR

D64927.

RefSeq

NP_416207.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NPD	X-ray	2.30	A/B	1-288	[»]
1O9B	X-ray	2.50	A/B	1-288	[»]
1VI2	X-ray	2.10	A/B	2-288	[»]

ProteinModelPortal

P0A6D5.

SMR

P0A6D5. Positions 5-288.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47967N.

IntAct

P0A6D5. 3 interactions.

MINT

MINT-1283305.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000278; EBESCP00000000278; EBESCG00000000231.
EBESCT00000015596; EBESCP00000014887; EBESCG00000014656.

GeneID

946200.

GenomeReviews

Gene locus JW1682 in contig AP009048_GR.
Gene locus b1692 in contig U00096_GR.

KEGG

ecj:JW1682.
eco:b1692.

PATRIC

32118690. VBIEscCol129921_1763.

Organism-specific databases

EchoBASE

EB1216.

EcoGene

EG11234. ydiB.

Phylogenomic databases

eggNOG

COG0169.

GeneTree

EBGT00050000010797.

HOGENOM

HBG553408.

OMA

GSFAMPA.

PhylomeDB

P0A6D5.

ProtClustDB

PRK12749.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11234-MONOMER.
MetaCyc:EG11234-MONOMER.

Gene expression databases

Genevestigator

P0A6D5.

Family and domain databases

HAMAP

MF_01578. Shikimate_DH_YdiB.
[Tree]

InterPro

IPR016040. NAD(P)-bd_dom.
IPR022872. Quinate/Shikimate_DH.
IPR013708. Shikimate_DH-bd_N.
IPR022893. Shikimate_quinate_DH.
IPR006151. Shikm_DH/Glu-tRNA_Rdtase.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

KO

K05887.

Pfam

PF01488. Shikimate_DH. 1 hit.
PF08501. Shikimate_dh_N. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

YDIB_ECOLI

Accession

Primary (citable) accession number: P0A6D5
Secondary accession number(s): P28244, P77647

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	January 25, 2012
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program