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P10724

- ALR_GEOSE

UniProt

P10724 - ALR_GEOSE

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Protein

Alanine racemase

Gene

alr

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.2 Publications

Catalytic activityi

L-alanine = D-alanine.3 PublicationsUniRule annotation

Cofactori

Pyridoxal phosphate.6 PublicationsUniRule annotation

Enzyme regulationi

Inhibited by acetate and propionate. Irreversibly inhibited by cycloserine.3 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei39 – 391Proton acceptor; specific for D-alanine
Binding sitei136 – 1361Substrate
Active sitei265 – 2651Proton acceptor; specific for L-alanine
Binding sitei312 – 3121Substrate; via amide nitrogen

GO - Molecular functioni

  1. alanine racemase activity Source: UniProtKB-HAMAP
  2. pyridoxal phosphate binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. D-alanine biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

SABIO-RKP10724.
UniPathwayiUPA00042; UER00497.

Names & Taxonomyi

Protein namesi
Recommended name:
Alanine racemaseUniRule annotation (EC:5.1.1.1UniRule annotation)
Gene namesi
Name:alr
Synonyms:dal
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi39 – 391K → A: Loss of activity. 1 Publication
Mutagenesisi166 – 1661H → A: 6.5-fold decrease in activity. 1 Publication
Mutagenesisi219 – 2191R → A: 100-fold decrease in activity. 1 Publication
Mutagenesisi219 – 2191R → E: 1000-fold decrease in activity. 1 Publication
Mutagenesisi219 – 2191R → K: 4-fold decrease in activity. 1 Publication
Mutagenesisi265 – 2651Y → A: 5000-fold decrease in activity. 1 Publication
Mutagenesisi265 – 2651Y → F: Loss of activity. 1 Publication
Mutagenesisi265 – 2651Y → S: 2000-fold decrease in activity. 1 Publication
Mutagenesisi354 – 3541Y → A: 54-fold increase in serine racemase activity. 1 Publication
Mutagenesisi354 – 3541Y → N: 81-fold increase in serine racemase activity. 1 Publication
Mutagenesisi354 – 3541Y → Q: 51-fold increase in serine racemase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 388388Alanine racemasePRO_0000114499Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei39 – 391N6-(pyridoxal phosphate)lysine
Modified residuei129 – 1291N6-carboxylysine5 Publications

Interactioni

Subunit structurei

Homodimer.5 Publications

Structurei

Secondary structure

1
388
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 138
Helixi14 – 2714
Beta strandi33 – 375
Helixi39 – 435
Helixi47 – 5711
Beta strandi61 – 666
Helixi67 – 759
Beta strandi82 – 843
Helixi90 – 923
Helixi93 – 986
Beta strandi101 – 1055
Helixi108 – 11710
Beta strandi124 – 1307
Beta strandi132 – 1343
Beta strandi136 – 1394
Helixi142 – 15413
Beta strandi158 – 1647
Beta strandi172 – 1743
Helixi176 – 18914
Beta strandi192 – 1943
Beta strandi197 – 2004
Helixi204 – 2096
Helixi211 – 2133
Beta strandi217 – 2204
Helixi222 – 2254
Helixi231 – 2366
Beta strandi245 – 2506
Beta strandi252 – 2576
Beta strandi262 – 2643
Helixi265 – 2673
Beta strandi273 – 2819
Helixi284 – 2863
Helixi290 – 2945
Beta strandi296 – 2994
Beta strandi302 – 3087
Beta strandi315 – 3184
Beta strandi328 – 3358
Beta strandi338 – 3403
Helixi342 – 3498
Helixi355 – 3595
Beta strandi366 – 3705
Beta strandi373 – 3786

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP10724.
SMRiP10724. Positions 2-382.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP10724.

Family & Domainsi

Sequence similaritiesi

Belongs to the alanine racemase family.UniRule annotation

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_01201. Ala_racemase.
InterProiIPR000821. 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]
PfamiPF00842. Ala_racemase_C. 1 hit.
PF01168. Ala_racemase_N. 1 hit.
[Graphical view]
PRINTSiPR00992. ALARACEMASE.
SMARTiSM01005. Ala_racemase_C. 1 hit.
[Graphical view]
SUPFAMiSSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR00492. alr. 1 hit.
PROSITEiPS00395. ALANINE_RACEMASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P10724-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNDFHRDTWA EVDLDAIYDN VENLRRLLPD DTHIMAVVKA NAYGHGDVQV
60 70 80 90 100
ARTALEAGAS RLAVAFLDEA LALREKGIEA PILVLGASRP ADAALAAQQR
110 120 130 140 150
IALTVFRSDW LEEASALYSG PFPIHFHLKM DTGMGRLGVK DEEETKRIVA
160 170 180 190 200
LIERHPHFVL EGLYTHFATA DEVNTDYFSY QYTRFLHMLE WLPSRPPLVH
210 220 230 240 250
CANSAASLRF PDRTFNMVRF GIAMYGLAPS PGIKPLLPYP LKEAFSLHSR
260 270 280 290 300
LVHVKKLQPG EKVSYGATYT AQTEEWIGTI PIGYADGWLR RLQHFHVLVD
310 320 330 340 350
GQKAPIVGRI CMDQCMIRLP GPLPVGTKVT LIGRQGDEVI SIDDVARHLE
360 370 380
TINYEVPCTI SYRVPRIFFR HKRIMEVRNA IGRGESSA
Length:388
Mass (Da):43,593
Last modified:November 1, 1997 - v2
Checksum:iF54AA581F135EA7A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti37 – 382VV → PP AA sequence (PubMed:3730360)Curated
Sequence conflicti57 – 626AGASRL → RGPPP in AAA22220. (PubMed:2835089)Curated
Sequence conflicti288 – 2892WL → V in AAA22220. (PubMed:2835089)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M19142 Genomic DNA. Translation: AAA22220.1.
PIRiA29984.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M19142 Genomic DNA. Translation: AAA22220.1 .
PIRi A29984.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
4ILS X-ray 2.50 A/B/C 1-388 [» ]
ProteinModelPortali P10724.
SMRi P10724. Positions 2-382.
ModBasei Search...
MobiDBi Search...

Chemistry

ChEMBLi CHEMBL1075086.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00042 ; UER00497 .
SABIO-RK P10724.

Miscellaneous databases

EvolutionaryTracei P10724.

Family and domain databases

Gene3Di 2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPi MF_01201. Ala_racemase.
InterProi IPR000821. 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 ]
Pfami PF00842. Ala_racemase_C. 1 hit.
PF01168. Ala_racemase_N. 1 hit.
[Graphical view ]
PRINTSi PR00992. ALARACEMASE.
SMARTi SM01005. Ala_racemase_C. 1 hit.
[Graphical view ]
SUPFAMi SSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsi TIGR00492. alr. 1 hit.
PROSITEi PS00395. ALANINE_RACEMASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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, CARBAMYLATION 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, CARBAMYLATION 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, CARBAMYLATION 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, CARBAMYLATION 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, CARBAMYLATION AT LYS-129.

Entry informationi

Entry nameiALR_GEOSE
AccessioniPrimary (citable) accession number: P10724
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: November 1, 1997
Last modified: October 29, 2014
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3