Reviewed, UniProtKB/Swiss-Prot P45510 (DHAK_CITFR)

Names and origin

Protein names

Recommended name:
    Dihydroxyacetone kinase
      Short name=DHA kinase
    EC=2.7.1.29
Alternative name(s):
    Glycerone kinase

Gene names

Name:

dhaK

Organism

Citrobacter freundii

Taxonomic identifier

546 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Citrobacter

Protein attributes

Sequence length	552 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	Catalyzes the phosphorylation of dihydroxyacetone.
Catalytic activity	ATP + glycerone = ADP + glycerone phosphate.
Cofactor	Magnesium. Calcium.
Pathway	Polyol metabolism; glycerol fermentation; glycerone phosphate from glycerol (oxidative route): step 2/2.
Subunit structure	Homodimer.
Domain	The C-terminal domain consists of a eight-helix alpha barrel. The eight helices form a pocket that includes a tightly bound phospholipid. The cellular function of this lipid is unknown.
Sequence similarities	Contains 1 DAK1 (dihydroxyacetone kinase subunit 1) domain. Contains 1 DAK2 (dihydroxyacetone kinase subunit 2) domain.
Biophysicochemical properties	Kinetic parameters: KM=30 µM for dihydroxyacetone KM=70 µM for ATP

Ontologies

Keywords
Biological process	Glycerol metabolism
Ligand	ATP-binding Calcium Lipid-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	glycerol metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW glycerone kinase activity Inferred from electronic annotation. Source: EC lipid binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 552

551

Dihydroxyacetone kinase

PRO_0000121528

Regions

Domain

19 – 331

313

DAK1

Domain

382 – 548

167

DAK2

Nucleotide binding

387 – 391

5

ATP

Nucleotide binding

431 – 476

46

ATP

Sites

Active site

220

1

Tele-hemiaminal-histidine intermediate

Metal binding

380

1

Magnesium 2

Metal binding

385

1

Magnesium 1

Metal binding

385

1

Magnesium 2

Metal binding

387

1

Magnesium 1

Metal binding

387

1

Magnesium 2

Metal binding

388

1

Magnesium 2

Binding site

61

1

Substrate

Binding site

114

1

Substrate

Binding site

533

1

ATP

Experimental info

Mutagenesis

380

1

D → A: Loss of kinase activity. Ref.2

Mutagenesis

385

1

D → A: Loss of kinase activity. Ref.2

Mutagenesis

387

1

D → A: Loss of kinase activity. Ref.2

Mutagenesis

388

1

T → H: Reduced kinase activity. Ref.2

Secondary structure

1

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552

Helix Strand Turn

Details...

Helix

9 – 11

3

Helix

12 – 22

11

Beta strand

29 – 32

4

Beta strand

40 – 44

5

Beta strand

52 – 61

10

Turn

62 – 65

4

Helix

66 – 68

3

Beta strand

73 – 82

10

Helix

88 – 98

11

Beta strand

104 – 110

7

Helix

112 – 127

16

Beta strand

132 – 137

6

Helix

155 – 167

13

Helix

172 – 184

13

Beta strand

186 – 194

9

Beta strand

203 – 205

3

Beta strand

213 – 215

3

Beta strand

225 – 229

5

Helix

233 – 247

15

Beta strand

254 – 260

7

Helix

266 – 277

12

Helix

282 – 284

3

Beta strand

285 – 292

8

Beta strand

300 – 309

10

Helix

314 – 319

6

Helix

356 – 371

16

Helix

373 – 381

9

Helix

388 – 404

17

Helix

413 – 427

15

Helix

430 – 448

19

Helix

453 – 468

16

Beta strand

474 – 476

3

Helix

478 – 490

13

Helix

495 – 511

17

Helix

529 – 531

3

Helix

534 – 547

14

Sequences

	Sequence		Length	Mass (Da)
	P45510-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 8208307ECF3F79EA	FASTA	552	57,940
	10 20 30 40 50 60 MSQFFFNQRT HLVSDVIDGA IIASPWNNLA RLESDPAIRI VVRRDLNKNN VAVISGGGSG 70 80 90 100 110 120 HEPAHVGFIG KGMLTAAVCG DVFASPSVDA VLTAIQAVTG EAGCLLIVKN YTGDRLNFGL 130 140 150 160 170 180 AAEKARRLGY NVEMLIVGDD ISLPDNKHPR GIAGTILVHK IAGYFAERGY NLATVLREAQ 190 200 210 220 230 240 YAASNTFSLG VALSSCHLPQ ETDAAPRHHP GHAELGMGIH GEPGASVIDT QNSAQVVNLM 250 260 270 280 290 300 VDKLLAALPE TGRLAVMINN LGGVSVAEMA IITRELASSP LHSRIDWLIG PASLVTALDM 310 320 330 340 350 360 KGFSLTAIVL EESIEKALLT EVETSNWPTP VPPREITCVV SSHASARVEF QPSANALVAG 370 380 390 400 410 420 IVELVTATLS DLETHLNALD AKVGDGDTGS TFAAAAREIA SLLHRQQLPL NNLATLFALI 430 440 450 460 470 480 GERLTVVMGG SSGVLMSIFF TAAGQKLEQG ANVVEALNTG LAQMKFYGGA DEGDRTMIDA 490 500 510 520 530 540 LQPALTSLLA QPKNLQAAFD AAQAGAERTC LSSKANAGRA SYLSSESLLG NMDPGAQRLA 550 MVFKALAESE LG

References

[1]

"Biochemical and molecular characterization of the oxidative branch of glycerol utilization by Citrobacter freundii." Daniel R., Stuertz K., Gottschalk G. J. Bacteriol. 177:4392-4401(1995) [PubMed: 7635824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-14, CHARACTERIZATION. Strain: ATCC 6750 / DSM 30040 / NCIB 8173 / M8BK.

[2]

"Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha-helical barrel ATP-binding domain." Siebold C., Arnold I., Garcia-Alles L.F., Baumann U., Erni B. J. Biol. Chem. 278:48236-48244(2003) [PubMed: 12966101] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH ATP; LIPID; DIHYDROXYACETONE AND MAGNESIUM IONS, MUTAGENESIS OF ASP-380; ASP-385; ASP-387 AND THR-388.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U09771 Genomic DNA. Translation: AAB48843.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UN8	X-ray	2.50	A/B	1-552	[»]
1UN9	X-ray	3.10	A/B	2-552	[»]

ModBase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MON-4504.

BRENDA

2.7.1.29. 2347.

Family and domain databases

InterPro

IPR004006. Dak1.
IPR004007. Dak2.
IPR012734. DhaK_ATP.
[Graphical view]

Pfam

PF02733. Dak1. 1 hit.
PF02734. Dak2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02361. dak_ATP. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DHAK_CITFR

Accession

Primary (citable) accession number: P45510

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 54 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)