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P10724 (ALR_GEOSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Alanine racemase

EC=5.1.1.1
Gene names
Name:alr
Synonyms:dal
OrganismGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifier1422 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Protein attributes

Sequence length388 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine. Ref.5 Ref.6

Catalytic activity

L-alanine = D-alanine. Ref.6 Ref.9 Ref.12

Cofactor

Pyridoxal phosphate. Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.13

Enzyme regulation

Inhibited by acetate and propionate. Irreversibly inhibited by cycloserine. Ref.9 Ref.12 Ref.13

Pathway

Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine from L-alanine: step 1/1. HAMAP-Rule MF_01201

Subunit structure

Homodimer. Ref.7 Ref.9 Ref.13

Sequence similarities

Belongs to the alanine racemase family.

Ontologies

Keywords
   LigandPyridoxal phosphate
   Molecular functionIsomerase
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processD-alanine biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

   Molecular_functionalanine racemase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

pyridoxal phosphate binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 388388Alanine racemase HAMAP-Rule MF_01201
PRO_0000114499

Sites

Active site391Proton acceptor; specific for D-alanine Ref.5 Ref.8 Ref.11 Ref.12 Ref.13
Active site2651Proton acceptor; specific for L-alanine Ref.5 Ref.8 Ref.11 Ref.12 Ref.13
Binding site1361Substrate
Binding site3121Substrate; via amide nitrogen

Amino acid modifications

Modified residue391N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_01201
Modified residue1291N6-carboxylysine HAMAP-Rule MF_01201

Experimental info

Mutagenesis391K → A: Loss of activity.
Mutagenesis1661H → A: 6.5-fold decrease in activity.
Mutagenesis2191R → A: 100-fold decrease in activity. Ref.4
Mutagenesis2191R → E: 1000-fold decrease in activity. Ref.4
Mutagenesis2191R → K: 4-fold decrease in activity. Ref.4
Mutagenesis2651Y → A: 5000-fold decrease in activity. Ref.13
Mutagenesis2651Y → F: Loss of activity. Ref.13
Mutagenesis2651Y → S: 2000-fold decrease in activity. Ref.13
Mutagenesis3541Y → A: 54-fold increase in serine racemase activity. Ref.6
Mutagenesis3541Y → N: 81-fold increase in serine racemase activity. Ref.6
Mutagenesis3541Y → Q: 51-fold increase in serine racemase activity. Ref.6
Sequence conflict37 – 382VV → PP AA sequence Ref.3
Sequence conflict57 – 626AGASRL → RGPPP in AAA22220. Ref.1
Sequence conflict288 – 2892WL → V in AAA22220. Ref.1

Secondary structure

................................................................................. 388
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P10724 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: F54AA581F135EA7A

FASTA38843,593
        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 

« Hide

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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M19142 Genomic DNA. Translation: AAA22220.1.
PIRA29984.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BD0X-ray1.60A/B1-388[»]
1EPVX-ray2.20A/B2-388[»]
1FTXX-ray2.20A/B2-388[»]
1L6FX-ray2.00A/B1-388[»]
1L6GX-ray2.00A/B1-388[»]
1NIUX-ray2.20A/B1-388[»]
1SFTX-ray1.90A/B1-388[»]
1XQKX-ray1.95A/B1-382[»]
1XQLX-ray1.80A/B1-382[»]
2SFPX-ray1.90A/B1-388[»]
3UW6X-ray2.30A/B/C1-388[»]
4ILSX-ray2.50A/B/C1-388[»]
ProteinModelPortalP10724.
SMRP10724. Positions 2-382.
ModBaseSearch...
MobiDBSearch...

Chemistry

ChEMBLCHEMBL1075086.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP10724.
UniPathwayUPA00042; UER00497.

Family and domain databases

Gene3D2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPMF_01201. Ala_racemase.
InterProIPR000821. Ala_racemase.
IPR009006. Ala_racemase/Decarboxylase_C.
IPR011079. Ala_racemase_C.
IPR001608. Ala_racemase_N.
IPR020622. Ala_racemase_pyridoxalP-BS.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamPF00842. Ala_racemase_C. 1 hit.
PF01168. Ala_racemase_N. 1 hit.
[Graphical view]
PRINTSPR00992. ALARACEMASE.
SMARTSM01005. Ala_racemase_C. 1 hit.
[Graphical view]
SUPFAMSSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsTIGR00492. alr. 1 hit.
PROSITEPS00395. ALANINE_RACEMASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP10724.

Entry information

Entry nameALR_GEOSE
AccessionPrimary (citable) accession number: P10724
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: November 1, 1997
Last modified: July 9, 2014
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways