PDBsum entry 1b8v

Go to PDB code: 
protein ligands links
Oxidoreductase PDB id
Protein chain
327 a.a. *
Waters ×127
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Malate dehydrogenase from aquaspirillum arcticum
Structure: Protein (malate dehydrogenase). Chain: a
Source: Aquaspirillum arcticum. Organism_taxid: 87645
Biol. unit: Dimer (from PDB file)
2.10Å     R-factor:   0.183    
Authors: S.Y.Kim,K.Y.Hwang,S.H.Kim,Y.S.Han,Y.Cho
Key ref:
S.Y.Kim et al. (1999). Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum. J Biol Chem, 274, 11761-11767. PubMed id: 10206992 DOI: 10.1074/jbc.274.17.11761
02-Feb-99     Release date:   09-Jul-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9ZF99  (MDH_AQUAR) -  Malate dehydrogenase
329 a.a.
327 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Malate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Citric acid cycle
      Reaction: (S)-malate + NAD+ = oxaloacetate + NADH
Bound ligand (Het Group name = NAD)
corresponds exactly
= oxaloacetate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1074/jbc.274.17.11761 J Biol Chem 274:11761-11767 (1999)
PubMed id: 10206992  
Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum.
S.Y.Kim, K.Y.Hwang, S.H.Kim, H.C.Sung, Y.S.Han, Y.Cho.
Aquaspillium arcticum is a psychrophilic bacterium that was isolated from arctic sediment and grows optimally at 4 degrees C. We have cloned, purified, and characterized malate dehydrogenase from A. arcticum (Aa MDH). We also have determined the crystal structures of apo-Aa MDH, Aa MDH.NADH binary complex, and Aa MDH.NAD.oxaloacetate ternary complex at 1.9-, 2.1-, and 2.5-A resolutions, respectively. The Aa MDH sequence is most closely related to the sequence of a thermophilic MDH from Thermus flavus (Tf MDH), showing 61% sequence identity and over 90% sequence similarity. Stability studies show that Aa MDH has a half-life of 10 min at 55 degrees C, whereas Tf MDH is fully active at 90 degrees C for 1 h. Aa MDH shows 2-3-fold higher catalytic efficiency compared with a mesophilic or a thermophilic MDH at the temperature range 4-10 degrees C. Structural comparison of Aa MDH and Tf MDH suggests that the increased relative flexibility of active site residues, favorable surface charge distribution for substrate and cofactor, and the reduced intersubunit ion pair interactions may be the major factors for the efficient catalytic activity of Aa MDH at low temperatures.
  Selected figure(s)  
Figure 2.
Fig. 2. a, a simulated annealed omit map around the NADH in Aa MDH·NADH complex. The map is shown with a contour level of 1 . b, a stereodiagram of the NADH binding site in Aa MDH. Important residues interacting with NADH are labeled, and distances between them are shown.
Figure 3.
Fig. 3. a, an omit map around the oxaloacetate in the Aa MDH ternary complex. The map is shown with a contour level of 1 . b, a stereodiagram of the oxaloacetate binding site in Aa MDH. Important residues interacting with oxaloacetate are labeled, and distances between them are shown.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 11761-11767) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20845078 Z.D.Wang, B.J.Wang, Y.D.Ge, W.Pan, J.Wang, L.Xu, A.M.Liu, and G.P.Zhu (2011).
Expression and identification of a thermostable malate dehydrogenase from multicellular prokaryote Streptomyces avermitilis MA-4680.
  Mol Biol Rep, 38, 1629-1636.  
20159163 B.Folch, Y.Dehouck, and M.Rooman (2010).
Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials.
  Biophys J, 98, 667-677.  
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
19152630 O.A.Adekoya, and I.Sylte (2009).
The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential.
  Chem Biol Drug Des, 73, 7.  
18655058 O.Almog, A.González, N.Godin, Leeuw, M.J.Mekel, D.Klein, S.Braun, G.Shoham, and R.L.Walter (2009).
The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state.
  Proteins, 74, 489-496.
PDB codes: 2gko 2ixt 3d43
19133128 R.P.Metpally, and B.V.Reddy (2009).
Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins.
  BMC Genomics, 10, 11.  
19011975 C.L.Goonasekara, and D.H.Heeley (2008).
Conformational properties of striated muscle tropomyosins from some salmonid fishes.
  J Muscle Res Cell Motil, 29, 135-143.  
18312599 C.Michaux, J.Massant, F.Kerff, J.M.Frère, J.D.Docquier, I.Vandenberghe, B.Samyn, A.Pierrard, G.Feller, P.Charlier, J.Van Beeumen, and J.Wouters (2008).
Crystal structure of a cold-adapted class C beta-lactamase.
  FEBS J, 275, 1687-1697.
PDB code: 2qz6
18203855 D.F.Rodrigues, and J.M.Tiedje (2008).
Coping with our cold planet.
  Appl Environ Microbiol, 74, 1677-1686.  
17510781 A.Rizzello, M.A.Ciardiello, R.Acierno, V.Carratore, T.Verri, G.di Prisco, C.Storelli, and M.Maffia (2007).
Biochemical characterization of a S-glutathionylated carbonic anhydrase isolated from gills of the Antarctic icefish Chionodraco hamatus.
  Protein J, 26, 335-348.  
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
17697122 D.Tronelli, E.Maugini, F.Bossa, and S.Pascarella (2007).
Structural adaptation to low temperatures--analysis of the subunit interface of oligomeric psychrophilic enzymes.
  FEBS J, 274, 4595-4608.  
17242507 E.K.Riise, M.S.Lorentzen, R.Helland, A.O.Smalås, H.K.Leiros, and N.P.Willassen (2007).
The first structure of a cold-active catalase from Vibrio salmonicida at 1.96 A reveals structural aspects of cold adaptation.
  Acta Crystallogr D Biol Crystallogr, 63, 135-148.
PDB code: 2isa
17195087 J.C.Marx, T.Collins, S.D'Amico, G.Feller, and C.Gerday (2007).
Cold-adapted enzymes from marine Antarctic microorganisms.
  Mar Biotechnol (NY), 9, 293-304.  
17098250 R.M.Robich, J.P.Rinehart, L.J.Kitchen, and D.L.Denlinger (2007).
Diapause-specific gene expression in the northern house mosquito, Culex pipiens L., identified by suppressive subtractive hybridization.
  J Insect Physiol, 53, 235-245.  
  18007057 T.Fujii, T.Oikawa, I.Muraoka, K.Soda, and Y.Hata (2007).
Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 983-986.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
  J Mol Model, 13, 485-497.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
  16511027 D.Dong, T.Ihara, H.Motoshima, and K.Watanabe (2005).
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 308-311.  
15670163 J.Arnórsdóttir, M.M.Kristjánsson, and R.Ficner (2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
  FEBS J, 272, 832-845.
PDB codes: 1s2n 1sh7
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
14975528 D.Georlette, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.Hoyoux, J.C.Marx, G.Sonan, G.Feller, and C.Gerday (2004).
Some like it cold: biocatalysis at low temperatures.
  FEMS Microbiol Rev, 28, 25-42.  
12831896 B.van den Burg (2003).
Extremophiles as a source for novel enzymes.
  Curr Opin Microbiol, 6, 213-218.  
15035024 G.Feller, and C.Gerday (2003).
Psychrophilic enzymes: hot topics in cold adaptation.
  Nat Rev Microbiol, 1, 200-208.  
12562783 H.Orikoshi, N.Baba, S.Nakayama, H.Kashu, K.Miyamoto, M.Yasuda, Y.Inamori, and H.Tsujibo (2003).
Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7.
  J Bacteriol, 185, 1153-1160.  
12876336 I.Leiros, E.Moe, O.Lanes, A.O.Smalås, and N.P.Willassen (2003).
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.
  Acta Crystallogr D Biol Crystallogr, 59, 1357-1365.
PDB code: 1okb
12577270 N.Aghajari, F.Van Petegem, V.Villeret, J.P.Chessa, C.Gerday, R.Haser, and J.Van Beeumen (2003).
Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
  Proteins, 50, 636-647.
PDB codes: 1g9k 1h71
  12113928 C.O.Brämer, and A.Steinbüchel (2002).
The malate dehydrogenase of Ralstonia eutropha and functionality of the C(3)/C(4) metabolism in a Tn5-induced mdh mutant.
  FEMS Microbiol Lett, 212, 159-164.  
12423352 J.Arnórsdottir, R.B.Smáradóttir, O.T.Magnússon, S.H.Thorbjarnardóttir, G.Eggertsson, and M.M.Kristjánsson (2002).
Characterization of a cloned subtilisin-like serine proteinase from a psychrotrophic Vibrio species.
  Eur J Biochem, 269, 5536-5546.  
11772602 K.L.Janiyani, and M.K.Ray (2002).
Cloning, sequencing, and expression of the cold-inducible hutU gene from the antarctic psychrotrophic bacterium Pseudomonas syringae.
  Appl Environ Microbiol, 68, 1.  
11985615 K.Mavromatis, I.Tsigos, M.Tzanodaskalaki, M.Kokkinidis, and V.Bouriotis (2002).
Exploring the role of a glycine cluster in cold adaptation of an alkaline phosphatase.
  Eur J Biochem, 269, 2330-2335.  
11589698 I.Tsigos, K.Mavromatis, M.Tzanodaskalaki, C.Pozidis, M.Kokkinidis, and V.Bouriotis (2001).
Engineering the properties of a cold active enzyme through rational redesign of the active site.
  Eur J Biochem, 268, 5074-5080.  
11160110 T.Lonhienne, K.Mavromatis, C.E.Vorgias, L.Buchon, C.Gerday, and V.Bouriotis (2001).
Cloning, sequences, and characterization of two chitinase genes from the Antarctic Arthrobacter sp. strain TAD20: isolation and partial characterization of the enzymes.
  J Bacteriol, 183, 1773-1779.  
10675897 C.Gerday, M.Aittaleb, M.Bentahir, J.P.Chessa, P.Claverie, T.Collins, S.D'Amico, J.Dumont, G.Garsoux, D.Georlette, A.Hoyoux, T.Lonhienne, M.A.Meuwis, and G.Feller (2000).
Cold-adapted enzymes: from fundamentals to biotechnology.
  Trends Biotechnol, 18, 103-107.  
10848966 D.Georlette, Z.O.Jónsson, F.Van Petegem, J.Chessa, J.Van Beeumen, U.Hübscher, and C.Gerday (2000).
A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures.
  Eur J Biochem, 267, 3502-3512.  
10899606 D.Kim, B.H.Kang, J.S.Han, and K.Y.Choi (2000).
Temperature and salt effects on proteolytic function of turnip mosaic potyvirus nuclear inclusion protein a exhibiting a low-temperature optimum activity.
  Biochim Biophys Acta, 1480, 29-40.  
10672012 H.K.Leiros, N.P.Willassen, and A.O.Smalås (2000).
Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation.
  Eur J Biochem, 267, 1039-1049.  
11026680 M.Mevarech, F.Frolow, and L.M.Gloss (2000).
Halophilic enzymes: proteins with a grain of salt.
  Biophys Chem, 86, 155-164.  
10672035 M.Rina, C.Pozidis, K.Mavromatis, M.Tzanodaskalaki, M.Kokkinidis, and V.Bouriotis (2000).
Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations.
  Eur J Biochem, 267, 1230-1238.  
11087953 N.Panasik, J.E.Brenchley, and G.K.Farber (2000).
Distributions of structural features contributing to thermostability in mesophilic and thermophilic alpha/beta barrel glycosyl hydrolases.
  Biochim Biophys Acta, 1543, 189-201.  
  11064190 Y.Okubo, K.Yokoigawa, N.Esaki, K.Soda, and H.Misono (2000).
High catalytic activity of alanine racemase from psychrophilic Bacillus psychrosaccharolyticus at high temperatures in the presence of pyridoxal 5'-phosphate.
  FEMS Microbiol Lett, 192, 169-173.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.