P42412 (IOLA_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Methylmalonate semialdehyde dehydrogenase [acylating]
Short name=MMSA dehydrogenase
Short name=MMSDH
Short name=MSDH
EC=1.2.1.27

Alternative name(s):
Malonate semialdehyde dehydrogenase [acetylating]
Short name=MSA dehydrogenase
EC=1.2.1.18

Gene names

Name:	iolA
Synonyms:	mmsA, yxdA
Ordered Locus Names:	BSU39760
ORF Names:	E83A

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	487 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Converts malonate semialdehyde (MSA) and methylmalonate semialdehyde (MMSA) into acetyl-CoA and propanoyl-CoA, respectively. Ref.4 Ref.5
Catalytic activity	3-oxopropanoate + CoA + NAD(P)+ = acetyl-CoA + CO2 + NAD(P)H. Ref.4 Ref.5 2-methyl-3-oxopropanoate + CoA + H2O + NAD+ = propanoyl-CoA + HCO3- + NADH. Ref.4 Ref.5
Pathway	Polyol metabolism; myo-inositol degradation into acetyl-CoA; acetyl-CoA from myo-inositol: step 7/7. HAMAP-Rule MF_01670
Subunit structure	Homotetramer. Ref.6
Sequence similarities	Belongs to the aldehyde dehydrogenase family. IolA subfamily.
Biophysicochemical properties	Kinetic parameters: KM=0.03 mM for CoA (with malonate semialdehyde at 30 degrees Celsius and pH 8.2) Ref.4 KM=0.6 mM for methylmalonate semialdehyde (at 30 degrees Celsius and pH 8.2) KM=0.12 mM for CoA (with methylmalonate semialdehyde at 30 degrees Celsius and pH 8.2) KM=0.12 mM for malonate semialdehyde (at 30 degrees Celsius and pH 8.2) KM=1.78 mM for NAD (with malonate semialdehyde at 30 degrees Celsius and pH 8.2) KM=2.3 mM for NAD (with methylmalonate semialdehyde at 30 degrees Celsius and pH 8.2)

Ontologies

Keywords
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	inositol catabolic process Inferred from electronic annotation. Source: HAMAP
Molecular_function	malonate-semialdehyde dehydrogenase (acetylating) activity Inferred from electronic annotation. Source: HAMAP methylmalonate-semialdehyde dehydrogenase (acylating) activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 487

487

Methylmalonate semialdehyde dehydrogenase [acylating] HAMAP-Rule MF_01670

PRO_0000056583

Regions

Nucleotide binding

176 – 180

5

NAD HAMAP-Rule MF_01670

Sites

Active site

284

1

Nucleophile

Binding site

382

1

NAD

Experimental info

Mutagenesis

36

1

C → A: No effect at either the structural or enzymatic levels; when associated with A-160; A-287; A-351 and A-413. Ref.4

Mutagenesis

160

1

C → A: No effect at either the structural or enzymatic levels when associated with A-36; A-287, A-351 and A-413. Ref.4

Mutagenesis

287

1

C → A: No effect at either the structural or enzymatic levels; when associated with A-36; A-160; A-351 and A-413. Ref.4

Mutagenesis

351

1

C → A: No effect at either the structural or enzymatic levels; when associated with A-36; A-160; A-287 and A-413. Ref.4

Mutagenesis

413

1

C → A: No effect at either the structural or enzymatic levels; when associated with A-36; A-160; A-287 and A-351. Ref.4

Secondary structure

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487

Helix Strand Turn

Details...

Beta strand

9 – 11

3

Beta strand

14 – 16

3

Beta strand

23 – 27

5

Turn

29 – 31

3

Beta strand

34 – 39

6

Helix

43 – 60

18

Helix

65 – 80

16

Helix

83 – 94

12

Helix

98 – 115

18

Helix

118 – 122

5

Beta strand

124 – 131

8

Beta strand

134 – 142

9

Beta strand

144 – 149

6

Helix

157 – 168

12

Beta strand

172 – 176

5

Beta strand

179 – 181

3

Helix

183 – 194

12

Beta strand

201 – 204

4

Helix

209 – 217

9

Beta strand

221 – 228

8

Helix

230 – 242

13

Beta strand

246 – 250

5

Beta strand

255 – 259

5

Helix

265 – 277

13

Helix

278 – 281

4

Beta strand

287 – 293

7

Helix

294 – 308

15

Helix

329 – 344

16

Beta strand

348 – 351

4

Beta strand

353 – 356

4

Beta strand

359 – 362

4

Beta strand

367 – 371

5

Helix

377 – 380

4

Beta strand

385 – 395

11

Helix

396 – 405

10

Beta strand

406 – 415

10

Helix

419 – 428

10

Beta strand

432 – 437

6

Beta strand

456 – 460

5

Helix

464 – 470

7

Beta strand

472 – 480

9

Sequences

	Sequence		Length	Mass (Da)
	P42412 [UniParc]. Last modified November 1, 1995. Version 1. Checksum: 412B63B05869229F	FASTA	487	53,453
	10 20 30 40 50 60 MAEIRKLKNY INGEWVESKT DQYEDVVNPA TKEVLCQVPI STKEDIDYAA QTAAEAFKTW 70 80 90 100 110 120 SKVAVPRRAR ILFNFQQLLS QHKEELAHLI TIENGKNTKE ALGEVGRGIE NVEFAAGAPS 130 140 150 160 170 180 LMMGDSLASI ATDVEAANYR YPIGVVGGIA PFNFPMMVPC WMFPMAIALG NTFILKPSER 190 200 210 220 230 240 TPLLTEKLVE LFEKAGLPKG VFNVVYGAHD VVNGILEHPE IKAISFVGSK PVGEYVYKKG 250 260 270 280 290 300 SENLKRVQSL TGAKNHTIVL NDANLEDTVT NIVGAAFGSA GERCMACAVV TVEEGIADEF 310 320 330 340 350 360 MAKLQEKVAD IKIGNGLDDG VFLGPVIRED NKKRTLSYIE KGLEEGARLV CDGRENVSDD 370 380 390 400 410 420 GYFVGPTIFD NVTTEMTIWK DEIFAPVLSV IRVKNLKEAI EIANKSEFAN GACLFTSNSN 430 440 450 460 470 480 AIRYFRENID AGMLGINLGV PAPMAFFPFS GWKSSFFGTL HANGKDSVDF YTRKKVVTAR YPAPDFN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of a 36-kb region of the Bacillus subtilis genome between the gnt and iol operons." Yoshida K., Seki S., Fujimura M., Miwa Y., Fujita Y. DNA Res. 2:61-69(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168 / BGSC1A1.
[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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[3]	"Cloning and nucleotide sequencing of a 15 kb region of the Bacillus subtilis genome containing the iol operon." Yoshida K., Sano H., Miwa Y., Ogasawara N., Fujita Y. Microbiology 140:2289-2298(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 71-487. Strain: 168 / BGSC1A1.
[4]	"Mechanistic characterization of the MSDH (methylmalonate semialdehyde dehydrogenase) from Bacillus subtilis." Stines-Chaumeil C., Talfournier F., Branlant G. Biochem. J. 395:107-115(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, MUTAGENESIS OF CYS-36; CYS-160; CYS-287; CYS-351 AND CYS-413, BIOPHYSICOCHEMICAL PROPERTIES.
[5]	"Myo-inositol catabolism in Bacillus subtilis." Yoshida K., Yamaguchi M., Morinaga T., Kinehara M., Ikeuchi M., Ashida H., Fujita Y. J. Biol. Chem. 283:10415-10424(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY. Strain: 168 / 60015.
[6]	"Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis." Dubourg H., Stines-Chaumeil C., Didierjean C., Talfournier F., Rahuel-Clermont S., Branlant G., Aubry A. Acta Crystallogr. D 60:1435-1437(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 2-487 IN COMPLEX WITH NAD, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB005554 Genomic DNA. Translation: BAA21609.1.
AL009126 Genomic DNA. Translation: CAB16012.1.
D14399 Genomic DNA. Translation: BAA03290.1.

PIR

A69645.

RefSeq

NP_391855.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1T90	X-ray	2.50	A/B/C/D	2-487	[»]

ProteinModelPortal

P42412.

SMR

P42412. Positions 3-486.

ModBase

Search...

Protein-protein interaction databases

STRING

224308.BSU39760.

Proteomic databases

PaxDb

P42412.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB16012; CAB16012; BSU39760.

GeneID

937575.

KEGG

bsu:BSU39760.

PATRIC

18980016. VBIBacSub10457_4170.

Organism-specific databases

GenoList

BSU39760. [Micado]

Phylogenomic databases

eggNOG

COG1012.

HOGENOM

HOG000271507.

KO

K00140.

OMA

TMLLVEL.

ProtClustDB

CLSK2460970.

Enzyme and pathway databases

BioCyc

BSUB:BSU39760-MONOMER.

UniPathway

UPA00076; UER00148.

Family and domain databases

Gene3D

3.40.309.10. 1 hit.
3.40.605.10. 1 hit.

HAMAP

MF_01670. IolA.

InterPro

IPR016161. Ald_DH/histidinol_DH.
IPR016163. Ald_DH_C.
IPR016160. Ald_DH_CS.
IPR016162. Ald_DH_N.
IPR015590. Aldehyde_DH_dom.
IPR010061. MeMal-semiAld_DH.
IPR023510. MeMal-semiAld_DH_GmP_bac.
[Graphical view]

PANTHER

PTHR11699:SF27. PTHR11699:SF27. 1 hit.

Pfam

PF00171. Aldedh. 1 hit.
[Graphical view]

SUPFAM

SSF53720. Aldehyde_DH/Histidinol_DH. 1 hit.

TIGRFAMs

TIGR01722. MMSDH. 1 hit.

PROSITE

PS00070. ALDEHYDE_DEHYDR_CYS. 1 hit.
PS00687. ALDEHYDE_DEHYDR_GLU. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P42412.

Entry information

Entry name

IOLA_BACSU

Accession

Primary (citable) accession number: P42412

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program