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P61889 (MDH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Malate dehydrogenase

EC=1.1.1.37
Gene names
Name:mdh
Ordered Locus Names:b3236, JW3205
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length312 AA.
Sequence statusComplete.
Protein existenceEvidence 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 312312Malate dehydrogenase HAMAP-Rule MF_01516
PRO_0000113301

Regions

Nucleotide binding7 – 137NAD HAMAP-Rule MF_01516
Nucleotide binding117 – 1193NAD HAMAP-Rule MF_01516

Sites

Active site1771Proton acceptor
Binding site341NAD
Binding site811Substrate
Binding site871Substrate
Binding site941NAD
Binding site1191Substrate
Binding site1531Substrate
Binding site2271NAD

Natural variations

Natural variant711D → N in strain: EC47, EC49, EC50 and RT272.
Natural variant1061A → S in strain: ECOR 27 and RT082.
Natural variant2091A → P in strain: MB001D.
Natural variant2181A → 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 variant2321A → T in strain: ECO R37.
Natural variant2491V → I in strain: RT083.
Natural variant2891Q → K in strain: EC35, EC38, EC40,EC44, EC46, EC47 and RT272.
Natural variant2901N → S in strain: E2666-74, ECOR 27, ECOR 45, RL012A, RT104 and RT174.
Natural variant2911A → S in strain: EC35.
Natural variant2941G → A in strain: ECOR 45.
Natural variant2971D → N in strain: E830587.

Experimental info

Mutagenesis1531R → C: Loss of interaction with substrate. Ref.19
Sequence conflict371P → S Ref.5
Sequence conflict701A → R Ref.2
Sequence conflict801A → R Ref.1
Sequence conflict801A → R Ref.2
Sequence conflict1161I → N Ref.2
Sequence conflict1441F → L Ref.1
Sequence conflict305 – 3128LGEEFVNK → WAKSSLISN Ref.2
Sequence conflict3071E → Q Ref.1

Secondary structure

................................................... 312
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P61889 [UniParc].

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

FASTA31232,337
        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' 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 277:1453-1462(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.
PIRDEECM. F65115.
RefSeqNP_417703.1. NC_000913.3.
YP_491420.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CMEmodel-A1-312[»]
1EMDX-ray1.90A1-312[»]
1IB6X-ray2.10A/B/C/D1-312[»]
1IE3X-ray2.50A/B/C/D1-312[»]
2CMDX-ray1.87A1-312[»]
2PWZX-ray2.20A/C/E/G1-312[»]
3HHPX-ray1.45A/B/C/D1-312[»]
ProteinModelPortalP61889.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-35924N.
IntActP61889. 10 interactions.

Chemistry

DrugBankDB00336. Nitrofurazone.

PTM databases

PhosSiteP0809413.

2D gel databases

SWISS-2DPAGEP61889.

Proteomic databases

PRIDEP61889.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76268; AAC76268; b3236.
BAE77279; BAE77279; BAE77279.
GeneID12931785.
947854.
KEGGecj:Y75_p3156.
eco:b3236.
PATRIC32121898. VBIEscCol129921_3333.

Organism-specific databases

EchoBASEEB0571.
EcoGeneEG10576. mdh.

Phylogenomic databases

KOK00024.
OMAKARGVYN.
OrthoDBEOG6091FG.
PhylomeDBP61889.

Enzyme and pathway databases

BioCycEcoCyc:MALATE-DEHASE-MONOMER.
ECOL316407:JW3205-MONOMER.
MetaCyc:MALATE-DEHASE-MONOMER.
SABIO-RKP61889.

Gene expression databases

GenevestigatorP61889.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPMF_01516. Malate_dehydrog_1.
InterProIPR001557. 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]
PANTHERPTHR11540. PTHR11540. 1 hit.
PfamPF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view]
PIRSFPIRSF000102. Lac_mal_DH. 1 hit.
SUPFAMSSF56327. SSF56327. 1 hit.
TIGRFAMsTIGR01772. MDH_euk_gproteo. 1 hit.
PROSITEPS00068. MDH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP61889.
PROP61889.

Entry information

Entry nameMDH_ECOLI
AccessionPrimary (citable) accession number: P61889
Secondary accession number(s): O30401 expand/collapse secondary AC list , O30402, O30403, P06994, Q2M8X7, Q59343, Q59344, Q59345, Q59346, Q59347, Q59348, Q60133, Q60150, Q933J3, Q93R02, Q9FDQ3, Q9FDQ4, Q9FDQ5
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: June 7, 2004
Last modified: July 9, 2014
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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