Alanine racemase, biosynthetic - Escherichia coli (strain K12)

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P0A6B4 (ALR1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 78. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Alanine racemase, biosynthetic
EC=5.1.1.1

Gene names

Name:	alr
Ordered Locus Names:	b4053, JW4013

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	359 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. Ref.7
Catalytic activity	L-alanine = D-alanine. Ref.7
Cofactor	Pyridoxal phosphate. Ref.7
Pathway	Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine from L-alanine: step 1/1. HAMAP-Rule MF_01201 Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_01201
Subunit structure	Homodimer. Ref.7
Sequence similarities	Belongs to the alanine racemase family.
Biophysicochemical properties	Kinetic parameters: K_M=0.31 mM for D-alanine Ref.7 K_M=1.00 mM for L-alanine

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Ligand	Pyridoxal phosphate
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
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 direct assay PubMed 15796715. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 359

359

Alanine racemase, biosynthetic HAMAP-Rule MF_01201

PRO_0000114514

Sites

Active site

Proton acceptor; specific for D-alanine

Active site

255

Proton acceptor; specific for L-alanine By similarity

Binding site

129

Substrate

Binding site

303

Substrate; via amide nitrogen

Amino acid modifications

Modified residue

N6-(pyridoxal phosphate)lysine By similarity

Modified residue

122

N6-carboxylysine HAMAP-Rule MF_01201

Experimental info

Mutagenesis

164

D → A: Slightly reduces affinity for D-Ala and L-Ala. Ref.7

Mutagenesis

164

D → K: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala. Ref.7

Mutagenesis

165

E → A: Slightly reduces affinity for D-Ala and L-Ala. Ref.7

Mutagenesis

165

E → K: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala. Ref.7

Mutagenesis

219

P → A: No effect on catalytic activity. No effect on affinity for D-Ala and L-Ala. Ref.7

Mutagenesis

221

E → A, K or P: Slightly increases catalytic activity. Slightly increases affinity for D-Ala and L-Ala. Ref.7

Secondary structure

359

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A6B4 [UniParc].

Last modified June 7, 2005. Version 1.
Checksum: FDE9B438115342C2
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FASTA

359

39,153

        10         20         30         40         50         60 
MQAATVVINR RALRHNLQRL RELAPASKMV AVVKANAYGH GLLETARTLP DADAFGVARL 

        70         80         90        100        110        120 
EEALRLRAGG ITKPVLLLEG FFDARDLPTI SAQHFHTAVH NEEQLAALEE ASLDEPVTVW 

       130        140        150        160        170        180 
MKLDTGMHRL GVRPEQAEAF YHRLTQCKNV RQPVNIVSHF ARADEPKCGA TEKQLAIFNT 

       190        200        210        220        230        240 
FCEGKPGQRS IAASGGILLW PQSHFDWVRP GIILYGVSPL EDRSTGADFG CQPVMSLTSS 

       250        260        270        280        290        300 
LIAVREHKAG EPVGYGGTWV SERDTRLGVV AMGYGDGYPR AAPSGTPVLV NGREVPIVGR 

       310        320        330        340        350 
VAMDMICVDL GPQAQDKAGD PVILWGEGLP VERIAEMTKV SAYELITRLT SRVAMKYVD

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The 92-min region of the Escherichia coli chromosome: location and cloning of the ubiA and alr genes." Lilley P.E., Stamford N.P., Vasudevan S.G., Dixon N.E. Gene 129:9-16(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Nucleotide sequence of dnaB and the primary structure of the dnaB protein from Escherichia coli." Nakayama N., Arai N., Bond M.W., Kaziro Y., Arai K. J. Biol. Chem. 259:97-101(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
[6]	"Aromatic amino acid aminotransferase of Escherichia coli: nucleotide sequence of the tyrB gene." Kuramitsu S., Inoue K., Ogawa T., Ogawa H., Kagamiyama H. Biochem. Biophys. Res. Commun. 133:134-139(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 320-359. Strain: K12.
[7]	"Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis." Wu D., Hu T., Zhang L., Chen J., Du J., Ding J., Jiang H., Shen X. Protein Sci. 17:1066-1076(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEXES WITH D-CYCLOSERINE AND PYRIDOXAL PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-34, MUTAGENESIS OF ASP-164; GLU-165; PRO-219 AND GLU-221, CARBOXYLATION AT LYS-122.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00006 Genomic DNA. Translation: AAC43147.1.
U00096 Genomic DNA. Translation: AAC77023.1.
AP009048 Genomic DNA. Translation: BAE78055.1.
K01174 Genomic DNA. No translation available.
M12047 Genomic DNA. No translation available.

PIR

PC1296. D65213.

RefSeq

NP_418477.1. NC_000913.2.
YP_492196.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2RJG	X-ray	2.40	A/B/C/D	1-359	[»]
2RJH	X-ray	2.40	A/B/C/D	1-359	[»]
3B8T	X-ray	3.00	A/B/C/D	1-359	[»]
3B8U	X-ray	3.00	A/B/C/D	1-359	[»]
3B8V	X-ray	2.60	A/B/C/D	1-359	[»]
3B8W	X-ray	2.70	A/B/C/D	1-359	[»]

ProteinModelPortal

P0A6B4.

SMR

P0A6B4. Positions 1-359.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A6B4. 6 interactions.

STRING

511145.b4053.

Proteomic databases

PaxDb

P0A6B4.

PRIDE

P0A6B4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77023; AAC77023; b4053.
BAE78055; BAE78055; BAE78055.

GeneID

12931829.
948564.

KEGG

ecj:Y75_p3940.
eco:b4053.

PATRIC

32123645. VBIEscCol129921_4171.

Organism-specific databases

EchoBASE

EB0001.

EcoGene

EG10001. alr.

Phylogenomic databases

eggNOG

COG0787.

HOGENOM

HOG000031446.

K01775.

OMA

HQLETAV.

ProtClustDB

PRK00053.

Enzyme and pathway databases

BioCyc

EcoCyc:ALARACEBIOSYN-MONOMER.
ECOL316407:JW4013-MONOMER.
MetaCyc:ALARACEBIOSYN-MONOMER.

SABIO-RK

P0A6B4.

UniPathway

UPA00042; UER00497.
UPA00219.

Gene expression databases

Genevestigator

P0A6B4.

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

BindingDB

P0A6B4.

ChEMBL

CHEMBL2833.

EvolutionaryTrace

P0A6B4.

Entry information

Entry name

ALR1_ECOLI

Accession

Primary (citable) accession number: P0A6B4
Secondary accession number(s): P29743, P78136, Q2M6Q1

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents