O34508 (AEEP_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
L-Ala-D/L-Glu epimerase
Short name=AE epimerase
Short name=AEE
EC=5.1.1.n1

Gene names

Name:	ykfB
Ordered Locus Names:	BSU12980

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	366 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of the other Ala-X dipeptides L-Ala-L-Asp, L-Ala-L-Leu, L-Ala-L-Met, and L-Ala-L-Ser. Is not able to epimerize other L-Ala-X dipeptides. Is also active with L-Ser-L-Glu and, oddly, L-Pro-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala. Ref.3 Ref.5
Catalytic activity	L-alanyl-D-glutamate = L-alanyl-L-glutamate. Ref.3
Cofactor	Binds 1 magnesium ion per subunit. Ref.6 Ref.7
Pathway	Cell wall degradation; peptidoglycan degradation.
Subunit structure	Homooctamer; tetramer of dimers. Ref.6
Induction	Repressed by AbrB, a transcription factor that negatively controls biofilm formation. Ref.4
Sequence similarities	Belongs to the mandelate racemase/muconate lactonizing enzyme family.
Biophysicochemical properties	Kinetic parameters: The catalytic efficiency is 25-fold higher with L-Ala-D-Glu than with L-Ala-D-Asp or L-Ala-D-Met as substrate. KM=320 µM for L-Ala-D-Glu (at pH 8.5) Ref.3 KM=28 µM for L-Ala-D-Asp (at pH 8.5) KM=510 µM for L-Ala-D-Met (at pH 8.5)

Ontologies

Keywords
Biological process	Cell wall biogenesis/degradation
Ligand	Magnesium Metal-binding
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cellular cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW racemase and epimerase activity, acting on amino acids and derivatives 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 – 366

366

L-Ala-D/L-Glu epimerase

PRO_0000388970

Sites

Active site

162

1

Proton acceptor; specific for (R)-substrate epimerization Ref.7

Active site

268

1

Proton acceptor; specific for (S)-substrate epimerization Ref.7

Metal binding

191

1

Magnesium

Metal binding

219

1

Magnesium

Metal binding

244

1

Magnesium

Binding site

24

1

Substrate

Binding site

135

1

Substrate

Binding site

160

1

Substrate

Binding site

296

1

Substrate; via carbonyl oxygen

Binding site

298

1

Substrate; via amide nitrogen

Binding site

321

1

Substrate

Binding site

323

1

Substrate

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

366

Helix Strand Turn

Details...

Beta strand

2 – 20

19

Beta strand

25 – 38

14

Turn

52 – 54

3

Helix

59 – 68

10

Helix

70 – 74

5

Helix

83 – 91

9

Helix

97 – 108

12

Turn

112 – 114

3

Helix

119 – 122

4

Beta strand

128 – 132

5

Beta strand

134 – 136

3

Helix

141 – 153

13

Beta strand

158 – 162

5

Helix

168 – 181

14

Beta strand

186 – 191

6

Helix

198 – 210

13

Beta strand

217 – 219

3

Helix

231 – 236

6

Beta strand

241 – 243

3

Helix

250 – 259

10

Beta strand

263 – 266

4

Turn

269 – 271

3

Helix

279 – 287

9

Beta strand

291 – 294

4

Helix

305 – 313

9

Beta strand

317 – 320

4

Helix

324 – 327

4

Beta strand

328 – 330

3

Beta strand

343 – 345

3

Sequences

	Sequence		Length	Mass (Da)
	O34508 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: 8E33E7955435CE8B	FASTA	366	39,473
	10 20 30 40 50 60 MKIIRIETSR IAVPLTKPFK TALRTVYTAE SVIVRITYDS GAVGWGEAPP TLVITGDSMD 70 80 90 100 110 120 SIESAIHHVL KPALLGKSLA GYEAILHDIQ HLLTGNMSAK AAVEMALYDG WAQMCGLPLY 130 140 150 160 170 180 QMLGGYRDTL ETDYTVSVNS PEEMAADAEN YLKQGFQTLK IKVGKDDIAT DIARIQEIRK 190 200 210 220 230 240 RVGSAVKLRL DANQGWRPKE AVTAIRKMED AGLGIELVEQ PVHKDDLAGL KKVTDATDTP 250 260 270 280 290 300 IMADESVFTP RQAFEVLQTR SADLINIKLM KAGGISGAEK INAMAEACGV ECMVGSMIET 310 320 330 340 350 360 KLGITAAAHF AASKRNITRF DFDAPLMLKT DVFNGGITYS GSTISMPGKP GLGIIGAALL KGEKEQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of the Bacillus subtilis genome between xlyA and ykoR." Devine K.M. Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168.
[2]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed: 9384377] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[3]	"Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases." Schmidt D.M.Z., Hubbard B.K., Gerlt J.A. Biochemistry 40:15707-15715(2001) [PubMed: 11747447] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, PROBABLE ROLE IN MUREIN PEPTIDE METABOLISM. Strain: 168.
[4]	"Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis." Hamon M.A., Stanley N.R., Britton R.A., Grossman A.D., Lazazzera B.A. Mol. Microbiol. 52:847-860(2004) [PubMed: 15101989] [Abstract] Cited for: INDUCTION.
[5]	"How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan)." Park J.T., Uehara T. Microbiol. Mol. Biol. Rev. 72:211-227(2008) [PubMed: 18535144] [Abstract] Cited for: PROBABLE FUNCTION IN PEPTIDOGLYCAN DEGRADATION, REVIEW.
[6]	"Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis." Gulick A.M., Schmidt D.M.Z., Gerlt J.A., Rayment I. Biochemistry 40:15716-15724(2001) [PubMed: 11747448] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR, SUBUNIT. Strain: 168.
[7]	"Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis." Klenchin V.A., Schmidt D.M.Z., Gerlt J.A., Rayment I. Biochemistry 43:10370-10378(2004) [PubMed: 15301535] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND MAGNESIUM, COFACTOR, ACTIVE SITES, REACTION MECHANISM. Strain: 168.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ002571 Genomic DNA. Translation: CAA05578.1.
AL009126 Genomic DNA. Translation: CAB13155.1.

PIR

H69855.

RefSeq

NP_389181.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JPM	X-ray	2.25	A/B/C/D	1-366	[»]
1TKK	X-ray	2.10	A/B/C/D/E/F/G/H	1-366	[»]

ProteinModelPortal

O34508.

SMR

O34508. Positions 1-359.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBBACT00000001248; EBBACP00000001248; EBBACG00000001246.

GeneID

939862.

GenomeReviews

Gene locus BSU12980 in contig AL009126_GR.

KEGG

bsu:BSU12980.

NMPDR

fig|224308.1.peg.1300.

PATRIC

18974353. VBIBacSub10457_1369.

Organism-specific databases

GenoList

BSU12980.

Phylogenomic databases

GeneTree

EBGT00050000001324.

HOGENOM

HBG450298.

OMA

LYADANE.

PhylomeDB

O34508.

ProtClustDB

CLSK887157.

Enzyme and pathway databases

BioCyc

BSUB:BSU12980-MONOMER.

Family and domain databases

InterPro

IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N.
IPR001354. MR_MLE.
[Graphical view]

PANTHER

PTHR13794. MR_MLE. 1 hit.

Pfam

PF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]

SMART

SM00922. MR_MLE. 1 hit.
[Graphical view]

PROSITE

PS00908. MR_MLE_1. False negative.
PS00909. MR_MLE_2. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

AEEP_BACSU

Accession

Primary (citable) accession number: O34508
Secondary accession number(s): Q796M5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 24, 2009
Last sequence update:	January 1, 1998
Last modified:	January 25, 2012
This is version 64 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program