Reviewed, UniProtKB/Swiss-Prot P10724 (ALR_BACST)

Names and origin

Protein names

Recommended name:
    Alanine racemase
    EC=5.1.1.1

Gene names

Name:	alr
Synonyms:	dal

Organism

Bacillus stearothermophilus (Geobacillus stearothermophilus)

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	388 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Provides the D-alanine required for cell wall biosynthesis. HAMAP MF_01201
Catalytic activity	L-alanine = D-alanine. HAMAP MF_01201
Cofactor	Pyridoxal phosphate. HAMAP MF_01201
Pathway	Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine from L-alanine: step 1/1. HAMAP MF_01201 Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_01201
Subunit structure	Homodimer. HAMAP MF_01201
Sequence similarities	Belongs to the alanine racemase family.

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Ligand	Pyridoxal phosphate
Molecular function	Isomerase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	alanine metabolic process Inferred from electronic annotation. Source: HAMAP cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	alanine racemase activity Inferred from electronic annotation. Source: HAMAP pyridoxal phosphate binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 388

388

Alanine racemase HAMAP MF_01201

PRO_0000114499

Sites

Active site

39

1

Proton acceptor; specific for D-alanine Ref.8

Active site

265

1

Proton acceptor; specific for L-alanine Ref.8

Amino acid modifications

Modified residue

39

1

N6-(pyridoxal phosphate)lysine

Experimental info

Mutagenesis

39

1

K → A: Loss of activity. HAMAP MF_01201

Mutagenesis

166

1

H → A: 6.5-fold decrease in activity. HAMAP MF_01201

Mutagenesis

219

1

R → A: 100-fold decrease in activity. Ref.7

Mutagenesis

219

1

R → E: 1000-fold decrease in activity. Ref.7

Mutagenesis

219

1

R → K: 4-fold decrease in activity. Ref.7

Mutagenesis

265

1

Y → A: 5000-fold decrease in activity. HAMAP MF_01201

Mutagenesis

265

1

Y → F: Loss of activity. HAMAP MF_01201

Mutagenesis

265

1

Y → S: 2000-fold decrease in activity. HAMAP MF_01201

Sequence conflict

37 – 38

2

VV → PP AA sequence Ref.3

Sequence conflict

57 – 62

6

AGASRL → RGPPP in AAA22220. Ref.1

Sequence conflict

288 – 289

2

WL → V in AAA22220. Ref.1

Secondary structure

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388

Helix Strand Turn

Details...

Beta strand

6 – 13

8

Helix

14 – 27

14

Beta strand

33 – 37

5

Helix

39 – 43

5

Helix

47 – 57

11

Beta strand

61 – 66

6

Helix

67 – 75

9

Beta strand

82 – 84

3

Helix

90 – 92

3

Helix

93 – 98

6

Beta strand

101 – 105

5

Helix

108 – 117

10

Beta strand

124 – 130

7

Beta strand

132 – 134

3

Beta strand

136 – 139

4

Helix

142 – 154

13

Beta strand

158 – 164

7

Helix

176 – 189

14

Beta strand

197 – 200

4

Helix

204 – 209

6

Beta strand

217 – 220

4

Helix

222 – 225

4

Helix

231 – 236

6

Beta strand

245 – 250

6

Beta strand

252 – 257

6

Beta strand

262 – 264

3

Helix

265 – 267

3

Beta strand

273 – 281

9

Helix

284 – 286

3

Helix

290 – 294

5

Beta strand

296 – 299

4

Beta strand

302 – 308

7

Beta strand

315 – 318

4

Beta strand

328 – 335

8

Beta strand

338 – 340

3

Helix

342 – 349

8

Helix

355 – 359

5

Beta strand

366 – 370

5

Beta strand

373 – 378

6

Sequences

	Sequence		Length	Mass (Da)
	P10724-1 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: F54AA581F135EA7A	FASTA	388	43,593
	10 20 30 40 50 60 MNDFHRDTWA EVDLDAIYDN VENLRRLLPD DTHIMAVVKA NAYGHGDVQV ARTALEAGAS 70 80 90 100 110 120 RLAVAFLDEA LALREKGIEA PILVLGASRP ADAALAAQQR IALTVFRSDW LEEASALYSG 130 140 150 160 170 180 PFPIHFHLKM DTGMGRLGVK DEEETKRIVA LIERHPHFVL EGLYTHFATA DEVNTDYFSY 190 200 210 220 230 240 QYTRFLHMLE WLPSRPPLVH CANSAASLRF PDRTFNMVRF GIAMYGLAPS PGIKPLLPYP 250 260 270 280 290 300 LKEAFSLHSR LVHVKKLQPG EKVSYGATYT AQTEEWIGTI PIGYADGWLR RLQHFHVLVD 310 320 330 340 350 360 GQKAPIVGRI CMDQCMIRLP GPLPVGTKVT LIGRQGDEVI SIDDVARHLE TINYEVPCTI 370 380 SYRVPRIFFR HKRIMEVRNA IGRGESSA

References

[1]	"Thermostable alanine racemase from Bacillus stearothermophilus: DNA and protein sequence determination and secondary structure prediction." Tanizawa K., Ohshima A., Scheidegger A., Inagaki K., Tanaka H., Soda K. Biochemistry 27:1311-1316(1988) [PubMed: 2835089] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Mechanism of inactivation of alanine racemase by beta, beta, beta-trifluoroalanine." Faraci W.S., Walsh C.T. Biochemistry 28:431-437(1989) [PubMed: 2496744] [Abstract] Cited for: PROTEIN SEQUENCE OF 31-43.
[3]	"Time-dependent inhibition of Bacillus stearothermophilus alanine racemase by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate complexes." Badet B., Inagaki K., Soda K., Walsh C.T. Biochemistry 25:3275-3282(1986) [PubMed: 3730360] [Abstract] Cited for: PROTEIN SEQUENCE OF 36-43.
[4]	"Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution." Shaw J.P., Petsko G.A., Ringe D. Biochemistry 36:1329-1342(1997) [PubMed: 9063881] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SEQUENCE REVISION.
[5]	"Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine." Stamper C.G., Morollo A.A., Ringe D. Biochemistry 37:10438-10445(1998) [PubMed: 9671513] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
[6]	"Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase." Morollo A.A., Petsko G.A., Ringe D. Biochemistry 38:3293-3301(1999) [PubMed: 10079072] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). Strain: ATCC 12980 / DSM 22 / IFO 12550 / NCIB 8923 / NCTC 10339.
[7]	"Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase." Sun S., Toney M.D. Biochemistry 38:4058-4065(1999) [PubMed: 10194319] [Abstract] Cited for: MUTAGENESIS OF ARG-219.
[8]	"Tyrosine 265 of alanine racemase serves as a base abstracting alpha-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to D-alanine." Watanabe A., Yoshimura T., Mikami B., Esaki N. J. Biochem. 126:781-786(1999) [PubMed: 10502689] [Abstract] Cited for: ACTIVE SITES, MUTAGENESIS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M19142 Genomic DNA. Translation: AAA22220.1.

PIR

A29984.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BD0	X-ray	1.60	A/B	1-388	[»]
1EPV	X-ray	2.20	A/B	2-388	[»]
1FTX	X-ray	2.20	A/B	2-388	[»]
1L6F	X-ray	2.00	A/B	1-388	[»]
1L6G	X-ray	2.00	A/B	1-388	[»]
1NIU	X-ray	2.20	A/B	1-388	[»]
1SFT	X-ray	1.90	A/B	1-388	[»]
1XQK	X-ray	1.95	A/B	1-382	[»]
1XQL	X-ray	1.80	A/B	1-382	[»]
2SFP	X-ray	1.90	A/B	1-388	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

5.1.1.1. 266715.

Family and domain databases

HAMAP

MF_01201.
[Tree]

InterPro

IPR011079. Ala_racemase_C.
IPR001608. Ala_racemase_N.
IPR000821. Ala_racemase_reg.
[Graphical view]

Pfam

PF00842. Ala_racemase_C. 1 hit.
PF01168. Ala_racemase_N. 1 hit.
[Graphical view]

PRINTS

PR00992. ALARACEMASE.

TIGRFAMs

TIGR00492. alr. 1 hit.

PROSITE

PS00395. ALANINE_RACEMASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

ALR_BACST

Accession

Primary (citable) accession number: P10724

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 88 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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