P10724 (ALR_GEOSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Alanine racemase
EC=5.1.1.1

Gene names

Name:	alr
Synonyms:	dal

Organism

Geobacillus stearothermophilus (Bacillus stearothermophilus)

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	388 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.
Catalytic activity	L-alanine = D-alanine. HAMAP-Rule MF_01201
Cofactor	Pyridoxal phosphate.
Enzyme regulation	Inhibited by acetate and propionate. Irreversibly inhibited by cycloserine.
Pathway	Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine from L-alanine: step 1/1. HAMAP-Rule MF_01201
Subunit structure	Homodimer.
Sequence similarities	Belongs to the alanine racemase family.

Ontologies

Keywords
Ligand	Pyridoxal phosphate
Molecular function	Isomerase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	D-alanine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	alanine racemase activity Inferred from electronic annotation. Source: EC
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-Rule MF_01201

PRO_0000114499

Sites

Active site

39

1

Proton acceptor; specific for D-alanine Ref.5

Active site

265

1

Proton acceptor; specific for L-alanine Ref.5

Binding site

136

1

Substrate

Binding site

312

1

Substrate; via amide nitrogen

Amino acid modifications

Modified residue

39

1

N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_01201

Modified residue

129

1

N6-carboxylysine

Experimental info

Mutagenesis

39

1

K → A: Loss of activity.

Mutagenesis

166

1

H → A: 6.5-fold decrease in activity.

Mutagenesis

219

1

R → A: 100-fold decrease in activity. Ref.4

Mutagenesis

219

1

R → E: 1000-fold decrease in activity. Ref.4

Mutagenesis

219

1

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

Mutagenesis

265

1

Y → A: 5000-fold decrease in activity.

Mutagenesis

265

1

Y → F: Loss of activity.

Mutagenesis

265

1

Y → S: 2000-fold decrease in activity.

Mutagenesis

354

1

Y → A: 54-fold increase in serine racemase activity.

Mutagenesis

354

1

Y → N: 81-fold increase in serine racemase activity.

Mutagenesis

354

1

Y → Q: 51-fold increase in serine racemase activity.

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

Beta strand

172 – 174

3

Helix

176 – 189

14

Beta strand

192 – 194

3

Beta strand

197 – 200

4

Helix

204 – 209

6

Helix

211 – 213

3

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 [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 36-43.
[4]	"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] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-219.
[5]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION, ACTIVE SITES, MUTAGENESIS.
[6]	"Site-directed mutagenesis of Tyr354 in Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance." Patrick W.M., Weisner J., Blackburn J.M. ChemBioChem 3:789-792(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF TYR-354.
[7]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39, SEQUENCE REVISION.
[8]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND L-ALA PHOSPHONATE, COFACTOR, ACTIVE SITE.
[9]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS)IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND PROPIONATE, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR, PYRIDOXAL PHOSPHATE AT LYS-39, ENZYME REGULATION, CARBOXYLATION AT LYS-129. Strain: ATCC 12980 / DSM 22 / JCM 2501 / NBRC 12550 / NCIMB 8923 / NCTC 10339 / VKM B-510.
[10]	"Crystal stucture of alanine racemase in complex with D-alanine phosphonate." Stamper G.F., Ringe D. Submitted (SEP-2000) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH D-ALANINE PHOSPHONATE, CARBOXYLATION AT LYS-129.
[11]	"Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine." Watanabe A., Yoshimura T., Mikami B., Hayashi H., Kagamiyama H., Esaki N. J. Biol. Chem. 277:19166-19172(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE AND N-(5'-PHOSPHOPYRIDOXYL)-L-ALANINE, COFACTOR, ACTIVE SITE, PYRIDOXAL PHOSPHATE AT LYS-39, CARBOXYLATION AT LYS-129.
[12]	"A side reaction of alanine racemase: transamination of cycloserine." Fenn T.D., Stamper G.F., Morollo A.A., Ringe D. Biochemistry 42:5775-5783(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL PHOSPHATE AND CYCLOSERINE, CATALYTIC ACTIVITY, ENZYME REGULATION, COFACTOR, ACTIVE SITE, CARBOXYLATION AT LYS-129.
[13]	"Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase." Fenn T.D., Holyoak T., Stamper G.F., Ringe D. Biochemistry 44:5317-5327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH CYCLOSERINE AND PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39, MUTAGENESIS OF TYR-265, ENZYME REGULATION, ACTIVE SITE, CARBOXYLATION AT LYS-129.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M19142 Genomic DNA. Translation: AAA22220.1.

PIR

A29984.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
3UW6	X-ray	2.30	A/B/C	1-388	[»]

ProteinModelPortal

P10724.

SMR

P10724. Positions 2-382.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P10724.

UniPathway

UPA00042; UER00497.

Family and domain databases

Gene3D

2.40.37.10. 1 hit.

HAMAP

MF_01201. Ala_racemase.

InterPro

IPR000821. Ala_racemase.
IPR009006. Ala_racemase/Decarboxylase_C.
IPR011079. Ala_racemase_C.
IPR001608. Ala_racemase_N.
IPR020622. Ala_racemase_pyridoxalP-BS.
[Graphical view]

Pfam

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

PRINTS

PR00992. ALARACEMASE.

SMART

SM01005. Ala_racemase_C. 1 hit.
[Graphical view]

SUPFAM

SSF50621. Racem_decarbox_C. 1 hit.

TIGRFAMs

TIGR00492. alr. 1 hit.

PROSITE

PS00395. ALANINE_RACEMASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChEMBL

CHEMBL1075086.

EvolutionaryTrace

P10724.

Entry information

Entry name

ALR_GEOSE

Accession

Primary (citable) accession number: P10724

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 108 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program