Malate dehydrogenase - Escherichia coli (strain K12)

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P61889 (MDH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 93. History...

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

Documents (3) |

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:
Malate dehydrogenase
EC=1.1.1.37

Gene names

Name:	mdh
Ordered Locus Names:	b3236, JW3205

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	312 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible oxidation of malate to oxaloacetate. HAMAP-Rule MF_01516
Catalytic activity	(S)-malate + NAD⁺ = oxaloacetate + NADH. HAMAP-Rule MF_01516
Subunit structure	Homodimer. Ref.17 Ref.18 Ref.19
Sequence similarities	Belongs to the LDH/MDH superfamily. MDH type 1 family.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	anaerobic respiration Inferred from direct assay Ref.5. Source: EcoliWiki cellular carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro fermentation Inferred from direct assay Ref.5. Source: EcoliWiki glycolysis Inferred from direct assay Ref.5. Source: EcoliWiki malate metabolic process Inferred from direct assay PubMed 4960671. Source: EcoliWiki tricarboxylic acid cycle Inferred from direct assay Ref.5. Source: EcoliWiki
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB extrinsic to membrane Inferred from direct assay PubMed 15976458. Source: EcoliWiki
Molecular_function	L-malate dehydrogenase activity Inferred from electronic annotation. Source: HAMAP malate dehydrogenase activity Inferred from direct assay Ref.5 PubMed 4960671. Source: EcoliWiki nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 312

312

Malate dehydrogenase HAMAP-Rule MF_01516

PRO_0000113301

Regions

Nucleotide binding

7 – 13

NAD HAMAP-Rule MF_01516

Nucleotide binding

117 – 119

NAD HAMAP-Rule MF_01516

Sites

Active site

177

Proton acceptor

Binding site

NAD

Binding site

Substrate

Binding site

Substrate

Binding site

NAD

Binding site

119

Substrate

Binding site

153

Substrate

Binding site

227

NAD

Natural variations

Natural variant

D → N in strain: EC47, EC49, EC50 and RT272.

Natural variant

106

A → S in strain: ECOR 27 and RT082.

Natural variant

209

A → P in strain: MB001D.

Natural variant

218

A → R in strain: A8190, E2666-74, E830587, E851819, E3406, EC10, EC14,EC32, EC35, EC38, EC40, EC44, EC46, EC47,EC49, EC50, EC52, EC58, E64 and EC70.

Natural variant

232

A → T in strain: ECO R37.

Natural variant

249

V → I in strain: RT083.

Natural variant

289

Q → K in strain: EC35, EC38, EC40,EC44, EC46, EC47 and RT272.

Natural variant

290

N → S in strain: E2666-74, ECOR 27, ECOR 45, RL012A, RT104 and RT174.

Natural variant

291

A → S in strain: EC35.

Natural variant

294

G → A in strain: ECOR 45.

Natural variant

297

D → N in strain: E830587.

Experimental info

Mutagenesis

153

R → C: Loss of interaction with substrate. Ref.19

Sequence conflict

P → S Ref.5

Sequence conflict

A → R Ref.2

Sequence conflict

A → R Ref.1

Sequence conflict

A → R Ref.2

Sequence conflict

116

I → N Ref.2

Sequence conflict

144

F → L Ref.1

Sequence conflict

305 – 312

LGEEFVNK → WAKSSLISN Ref.2

Sequence conflict

307

E → Q Ref.1

Secondary structure

312

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P61889 [UniParc].

Last modified June 7, 2004. Version 1.
Checksum: 17741A3B5AD068BA
Show »

FASTA

312

32,337

        10         20         30         40         50         60 
MKVAVLGAAG GIGQALALLL KTQLPSGSEL SLYDIAPVTP GVAVDLSHIP TAVKIKGFSG 

        70         80         90        100        110        120 
EDATPALEGA DVVLISAGVA RKPGMDRSDL FNVNAGIVKN LVQQVAKTCP KACIGIITNP 

       130        140        150        160        170        180 
VNTTVAIAAE VLKKAGVYDK NKLFGVTTLD IIRSNTFVAE LKGKQPGEVE VPVIGGHSGV 

       190        200        210        220        230        240 
TILPLLSQVP GVSFTEQEVA DLTKRIQNAG TEVVEAKAGG GSATLSMGQA AARFGLSLVR 

       250        260        270        280        290        300 
ALQGEQGVVE CAYVEGDGQY ARFFSQPLLL GKNGVEERKS IGTLSAFEQN ALEGMLDTLK 

       310 
KDIALGEEFV NK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of the Escherichia coli gene encoding malate dehydrogenase." McAlister-Henn L., Blaber M., Bradshaw R.A., Nisco S.J. Nucleic Acids Res. 15:4993-4993(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Cloning and sequence of the mdh structural gene of Escherichia coli coding for malate dehydrogenase." Vogel R.F., Entian K.-D., Mecke D. Arch. Microbiol. 149:36-42(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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]	"Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase." Sutherland P., McAlister-Henn L. J. Bacteriol. 163:1074-1079(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-40.
[6]	"Malate dehydrogenase: isolation from E. coli and comparison with the eukaryotic mitochondrial and cytoplasmic forms." Fernley R.T., Lentz S.R., Bradshaw R.A. Biosci. Rep. 1:497-507(1981) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-36.
[7]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-26. Strain: K12 / EMG2.
[8]	"Structural studies of malate dehydrogenases (MDHs): MDHs in Brevundimonas species are the first reported MDHs in Proteobacteria which resemble lactate dehydrogenases in primary structure." Charnock C. J. Bacteriol. 179:4066-4070(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-26.
[9]	"Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases." Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C. Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-16.
[10]	"Bacterial defense against aging: role of the Escherichia coli ArcA regulator in gene expression, readjusted energy flux and survival during stasis." Nystroem T., Larsson C., Gustafsson L. EMBO J. 15:3219-3228(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-13.
[11]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-11. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[12]	"Protein identification with N and C-terminal sequence tags in proteome projects." Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.-C., Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L., Hochstrasser D.F. J. Mol. Biol. 278:599-608(1998) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-4. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[13]	"Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica." Boyd E.F., Nelson K., Wang F.-S., Whittam T.S., Selander R.K. Proc. Natl. Acad. Sci. U.S.A. 91:1280-1284(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-299. Strain: Various strains.
[14]	"Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies." Pupo G.M., Karaolis D.K., Lan R., Reeves P.R. Infect. Immun. 65:2685-2692(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-299. Strain: Various strains.
[15]	"Population genetics of Escherichia coli in a natural population of native Australian rats." Pupo G.M., Lan R., Reeves P.R., Baverstock P.R. Environ. Microbiol. 2:594-610(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-299. Strain: Various strains.
[16]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[17]	"Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87-A resolution." Hall M.D., Levitt D.G., Banaszak L.J. J. Mol. Biol. 226:867-882(1992) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
[18]	"Crystal structure of a ternary complex of Escherichia coli malate dehydrogenase citrate and NAD at 1.9 A resolution." Hall M.D., Banaszak L.J. J. Mol. Biol. 232:213-222(1993) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NAD AND SUBSTRATE ANALOG, SUBUNIT.
[19]	"Structural analyses of a malate dehydrogenase with a variable active site." Bell J.K., Yennawar H.P., Wright S.K., Thompson J.R., Viola R.E., Banaszak L.J. J. Biol. Chem. 276:31156-31162(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH NAD AND SUBSTRATE ANALOG, SUBUNIT, MUTAGENESIS OF ARG-153.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y00129 Genomic DNA. Translation: CAA68326.1.
M24777 Unassigned DNA. Translation: AAA16107.1.
U18997 Genomic DNA. Translation: AAA58038.1.
U00096 Genomic DNA. Translation: AAC76268.1.
AP009048 Genomic DNA. Translation: BAE77279.1.
M10417 Genomic DNA. Translation: AAA24147.1.
U04742 Genomic DNA. Translation: AAC43730.1.
U04743 Genomic DNA. Translation: AAC43731.1.
U04744 Genomic DNA. Translation: AAC43732.1.
U04745 Genomic DNA. Translation: AAC43733.1.
U04746 Genomic DNA. Translation: AAC43734.1.
U04747 Genomic DNA. Translation: AAC43735.1.
U04748 Genomic DNA. Translation: AAC43736.1.
U04749 Genomic DNA. Translation: AAC43737.1.
U04750 Genomic DNA. Translation: AAC43738.1.
U04751 Genomic DNA. Translation: AAC43739.1.
U04752 Genomic DNA. Translation: AAC43740.1.
U04753 Genomic DNA. Translation: AAC43741.1.
U04754 Genomic DNA. Translation: AAC43742.1.
U04755 Genomic DNA. Translation: AAC43743.1.
U04756 Genomic DNA. Translation: AAC43744.1.
U04757 Genomic DNA. Translation: AAC43745.1.
U04758 Genomic DNA. Translation: AAC43746.1.
U04759 Genomic DNA. Translation: AAC43747.1.
U04760 Genomic DNA. Translation: AAC43748.1.
U04770 Genomic DNA. Translation: AAC43758.1.
AF004170 Genomic DNA. Translation: AAB87003.1.
AF004171 Genomic DNA. Translation: AAB87004.1.
AF004172 Genomic DNA. Translation: AAB87005.1.
AF004173 Genomic DNA. Translation: AAB87006.1.
AF004174 Genomic DNA. Translation: AAB87007.1.
AF004175 Genomic DNA. Translation: AAB87008.1.
AF004176 Genomic DNA. Translation: AAB87009.1.
AF004177 Genomic DNA. Translation: AAB87010.1.
AF004179 Genomic DNA. Translation: AAB87012.1.
AF004180 Genomic DNA. Translation: AAB87013.1.
AF004182 Genomic DNA. Translation: AAB87015.1.
AF004183 Genomic DNA. Translation: AAB87016.1.
AF004184 Genomic DNA. Translation: AAB87017.1.
AF004186 Genomic DNA. Translation: AAB87019.1.
AF004187 Genomic DNA. Translation: AAB87020.1.
AF004188 Genomic DNA. Translation: AAB87021.1.
AF004190 Genomic DNA. Translation: AAB87023.1.
AF004191 Genomic DNA. Translation: AAB87024.1.
AF004195 Genomic DNA. Translation: AAB87028.1.
AF004196 Genomic DNA. Translation: AAB87029.1.
AF004199 Genomic DNA. Translation: AAB87032.1.
AF004200 Genomic DNA. Translation: AAB87033.1.
AF004201 Genomic DNA. Translation: AAB87034.1.
AF004202 Genomic DNA. Translation: AAB87035.1.
AF004203 Genomic DNA. Translation: AAB87036.1.
AF004204 Genomic DNA. Translation: AAB87037.1.
AF004205 Genomic DNA. Translation: AAB87038.1.
AF004206 Genomic DNA. Translation: AAB87039.1.
AF004207 Genomic DNA. Translation: AAB87040.1.
AF004208 Genomic DNA. Translation: AAB87041.1.
AF004209 Genomic DNA. Translation: AAB87042.1.
AF091758 Genomic DNA. Translation: AAF97988.1.
AF091759 Genomic DNA. Translation: AAF97989.1.
AF091760 Genomic DNA. Translation: AAF97990.1.
AF091761 Genomic DNA. Translation: AAF97991.1.
AF091762 Genomic DNA. Translation: AAF97992.1.
AF091763 Genomic DNA. Translation: AAF97993.1.
AF091764 Genomic DNA. Translation: AAF97994.1.
AF091765 Genomic DNA. Translation: AAF97995.1.
AF091766 Genomic DNA. Translation: AAF97996.1.
AF091767 Genomic DNA. Translation: AAF97997.1.
AF091768 Genomic DNA. Translation: AAF97998.1.
AF091769 Genomic DNA. Translation: AAF97999.1.
AF091770 Genomic DNA. Translation: AAF98000.1.
AF091771 Genomic DNA. Translation: AAF98001.1.
AF091772 Genomic DNA. Translation: AAF98002.1.
AF091773 Genomic DNA. Translation: AAF98003.1.
AF091774 Genomic DNA. Translation: AAF98004.1.
AF091775 Genomic DNA. Translation: AAF98005.1.
AF091776 Genomic DNA. Translation: AAF98006.1.
AF091777 Genomic DNA. Translation: AAF98007.1.
AF091778 Genomic DNA. Translation: AAF98008.1.

PIR

DEECM. F65115.

RefSeq

NP_417703.1. NC_000913.2.
YP_491420.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CME	model	-	A	1-312	[»]
1EMD	X-ray	1.90	A	1-312	[»]
1IB6	X-ray	2.10	A/B/C/D	1-312	[»]
1IE3	X-ray	2.50	A/B/C/D	1-312	[»]
2CMD	X-ray	1.87	A	1-312	[»]
2PWZ	X-ray	2.20	A/C/E/G	1-312	[»]
3HHP	X-ray	1.45	A/B/C/D	1-312	[»]

ProteinModelPortal

P61889.

SMR

P61889. Positions 1-312.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35924N.

IntAct

P61889. 8 interactions.

PTM databases

PhosSite

P0809413.

2D gel databases

SWISS-2DPAGE

P61889.

Proteomic databases

PRIDE

P61889.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76268; AAC76268; b3236.
BAE77279; BAE77279; BAE77279.

GeneID

12931785.
947854.

KEGG

ecj:Y75_p3156.
eco:b3236.

PATRIC

32121898. VBIEscCol129921_3333.

Organism-specific databases

EchoBASE

EB0571.

EcoGene

EG10576. mdh.

Phylogenomic databases

K00024.

OMA

KNCPKAC.

ProtClustDB

PRK05086.

Enzyme and pathway databases

BioCyc

EcoCyc:MALATE-DEHASE-MONOMER.
ECOL316407:JW3205-MONOMER.
MetaCyc:MALATE-DEHASE-MONOMER.

SABIO-RK

P61889.

Gene expression databases

Genevestigator

P61889.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.
3.90.110.10. 1 hit.

HAMAP

MF_01516. Malate_dehydrog_1.

InterPro

IPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR001252. Malate_DH_AS.
IPR010097. Malate_DH_type1.
IPR023958. Malate_DH_type1_bac.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR11540. PTHR11540. 1 hit.

Pfam

PF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000102. Lac_mal_DH. 1 hit.

SUPFAM

SSF56327. Lactate_DH/Glyco_hydro_4_C. 1 hit.

TIGRFAMs

TIGR01772. MDH_euk_gproteo. 1 hit.

PROSITE

PS00068. MDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00336. Nitrofurazone.

EvolutionaryTrace

P61889.

Entry information

Entry name

MDH_ECOLI

Accession

Primary (citable) accession number: P61889
Secondary accession number(s): O30401

Q9FDQ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	June 7, 2004
Last modified:	May 1, 2013
This is version 93 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

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

Regions

Sites

Natural variations

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

2D gel 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