P19938 (DAAA_BACYM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-alanine aminotransferase
EC=2.6.1.21

Alternative name(s):
D-amino acid aminotransferase
D-amino acid transaminase
Short name=DAAT
D-aspartate aminotransferase

Gene names

Name:

dat

Organism

Bacillus sp. (strain YM-1)

Taxonomic identifier

72579 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	283 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	Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components. Ref.2 Ref.4
Catalytic activity	D-alanine + 2-oxoglutarate = pyruvate + D-glutamate. Ref.2 Ref.4
Cofactor	Pyridoxal phosphate. Ref.3
Subunit structure	Homodimer. Ref.2 Ref.3
Sequence similarities	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family.
Biophysicochemical properties	Absorption: Abs(max)=279 nm Ref.2 Holoenzyme exhibits additional strong peaks at 333 nm and 415 nm. Addition of D-alanine causes a decrease in absorbance at 419 nm and an increase at 335 nm. Kinetic parameters: KM=2.2 mM for D-alanine KM=5.9 mM for alpha-ketoglutarate KM=2.2 mM for alpha-ketobutyrate KM=2.2 mM for alpha-ketovalerate pH dependence: Optimum pH is 8.3. Temperature dependence: Optimum temperature is 60 degrees Celsius.

Ontologies

Keywords
Ligand	Pyridoxal phosphate
Molecular function	Aminotransferase Transferase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	D-amino acid biosynthetic process Inferred from direct assay Ref.2. Source: UniProtKB D-amino acid catabolic process Inferred from direct assay Ref.4. Source: UniProtKB
Molecular_function	D-alanine:2-oxoglutarate aminotransferase activity Inferred from direct assay Ref.2. Source: UniProtKB pyridoxal phosphate binding 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

Initiator methionine

1

1

Removed Ref.2

Chain

2 – 283

282

D-alanine aminotransferase

PRO_0000103248

Sites

Active site

146

1

Proton acceptor

Binding site

32

1

Substrate

Binding site

51

1

Pyridoxal phosphate

Binding site

99

1

Substrate

Binding site

101

1

Substrate

Binding site

178

1

Pyridoxal phosphate

Binding site

202

1

Pyridoxal phosphate

Amino acid modifications

Modified residue

146

1

N6-(pyridoxal phosphate)lysine

Experimental info

Mutagenesis

178

1

E → K: Loss of transaminase activity and small gain in racemase activity. Ref.6

Mutagenesis

202

1

L → A: Inactivates enzyme. Ref.5

Secondary structure

1

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283

Helix Strand Turn

Details...

Beta strand

3 – 6

4

Beta strand

9 – 12

4

Helix

13 – 15

3

Helix

23 – 26

4

Beta strand

30 – 38

9

Beta strand

41 – 44

4

Helix

45 – 58

14

Helix

67 – 81

15

Beta strand

85 – 94

10

Beta strand

111 – 118

8

Helix

123 – 128

6

Beta strand

130 – 136

7

Helix

151 – 162

12

Beta strand

166 – 172

7

Beta strand

175 – 179

5

Beta strand

182 – 188

7

Beta strand

191 – 194

4

Helix

205 – 216

12

Helix

228 – 232

5

Beta strand

235 – 241

7

Turn

242 – 244

3

Beta strand

245 – 252

8

Beta strand

255 – 257

3

Turn

258 – 260

3

Helix

264 – 274

11

Sequences

	Sequence		Length	Mass (Da)
	P19938 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 21563BDC35BE98F3	FASTA	283	32,396
	10 20 30 40 50 60 MGYTLWNDQI VKDEEVKIDK EDRGYQFGDG VYEVVKVYNG EMFTVNEHID RLYASAEKIR 70 80 90 100 110 120 ITIPYTKDKF HQLLHELVEK NELNTGHIYF QVTRGTSPRA HQFPENTVKP VIIGYTKENP 130 140 150 160 170 180 RPLENLEKGV KATFVEDIRW LRCDIKSLNL LGAVLAKQEA HEKGCYEAIL HRNNTVTEGS 190 200 210 220 230 240 SSNVFGIKDG ILYTHPANNM ILKGITRDVV IACANEINMP VKEIPFTTHE ALKMDELFVT 250 260 270 280 STTSEITPVI EIDGKLIRDG KVGEWTRKLQ KQFETKIPKP LHI

References

[1]	"The primary structure of thermostable D-amino acid aminotransferase from a thermophilic Bacillus species and its correlation with L-amino acid aminotransferases." Tanizawa K., Asano S., Masu Y., Kuramitsu S., Kagamiyama H., Tanaka H., Soda K. J. Biol. Chem. 264:2450-2454(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
[2]	"Thermostable D-amino acid aminotransferase from a thermophilic Bacillus species. Purification, characterization, and active site sequence determination." Tanizawa K., Masu Y., Asano S., Tanaka H., Soda K. J. Biol. Chem. 264:2445-2449(1989) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-21; 143-157 AND 281-283, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
[3]	"Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity." Sugio S., Petsko G.A., Manning J.M., Soda K., Ringe D. Biochemistry 34:9661-9669(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS), COFACTOR, SUBUNIT.
[4]	"Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase." Peisach D., Chipman D.M., van Ophem P.W., Manning J.M., Petsko G.A., Ringe D. Biochemistry 37:4958-4967(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY.
[5]	"Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0-A resolution: implication of the structural role of Leu201 in transamination." Sugio S., Kashima A., Kishimoto K., Peisach D., Petsko G.A., Ringe D., Yoshimura T., Esaki N. Protein Eng. 11:613-619(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), MUTAGENESIS OF LEU-202.
[6]	"Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity." van Ophem P.W., Peisach D., Erickson S.D., Soda K., Ringe D., Manning J.M. Biochemistry 38:1323-1331(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS), MUTAGENESIS OF GLU-178.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J04460 Genomic DNA. Translation: AAA22252.1.

PIR

A31422.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A0G	X-ray	2.00	A/B	2-283	[»]
1DAA	X-ray	1.94	A/B	2-283	[»]
1G2W	X-ray	2.00	A/B	2-283	[»]
2DAA	X-ray	2.10	A/B	2-282	[»]
2DAB	X-ray	2.00	A/B	2-283	[»]
3DAA	X-ray	1.90	A/B	2-278	[»]
3LQS	X-ray	1.90	A/B	2-281	[»]
4DAA	X-ray	2.40	A/B	2-278	[»]
5DAA	X-ray	2.90	A/B	2-278	[»]

ProteinModelPortal

P19938.

SMR

P19938. Positions 2-278.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P19938.

Family and domain databases

InterPro

IPR001544. Aminotrans_IV.
IPR018300. Aminotrans_IV_CS.
IPR005784. D_amino_transT.
[Graphical view]

PANTHER

PTHR11825. PTHR11825. 1 hit.

Pfam

PF01063. Aminotran_4. 1 hit.
[Graphical view]

SUPFAM

SSF56752. Aminotrans_IV. 1 hit.

TIGRFAMs

TIGR01121. D_amino_aminoT. 1 hit.

PROSITE

PS00770. AA_TRANSFER_CLASS_4. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P19938.

Entry information

Entry name

DAAA_BACYM

Accession

Primary (citable) accession number: P19938
Secondary accession number(s): P83771

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 89 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program