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(-) Description

Title :  STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
 
Authors :  B. Dalhus, M. Sarinen, U. H. Sauer, P. Eklund, K. Johansson, A. Karlsson, S. Ramaswamy, A. Bjork, B. Synstad, K. Naterstad, R. Sirevag, H. Eklund
Date :  04 Feb 02  (Deposition) - 15 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Dehydrogenase, Oxidoreductase, Tricarboxylic Acid Cycle, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dalhus, M. Saarinen, U. H. Sauer, P. Eklund, K. Johansson, A. Karlsson, S. Ramaswamy, A. Bjork, B. Synstad, K. Naterstad, R. Sirevag, H. Eklund
Structural Basis For Thermophilic Protein Stability: Structures Of Thermophilic And Mesophilic Malate Dehydrogenases
J. Mol. Biol. V. 318 707 2002
PubMed-ID: 12054817  |  Reference-DOI: 10.1016/S0022-2836(02)00050-5

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, C
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CHLOROFLEXUS AURANTIACUS
    Organism Taxid: 1108

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CD5Ligand/IonCADMIUM ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:165 , HOH A:2010 , HOH C:2106BINDING SITE FOR RESIDUE CD A1308
2AC2SOFTWAREGLU A:195 , GLU A:281 , HOH A:2097 , HOH A:2098 , GLU C:281 , HOH C:2124BINDING SITE FOR RESIDUE CD A1309
3AC3SOFTWAREASP A:200 , ASP A:243 , GLU A:277 , HOH A:2143BINDING SITE FOR RESIDUE CD A1310
4AC4SOFTWAREHOH A:2121 , HOH A:2123 , GLU C:165BINDING SITE FOR RESIDUE CD C1308
5AC5SOFTWAREGLU A:159 , GLU C:159 , HOH C:2064BINDING SITE FOR RESIDUE CD C1309
6AC6SOFTWAREGLY A:11 , PHE A:12 , VAL A:13 , ASP A:33 , ILE A:34 , VAL A:35 , SER A:78 , GLY A:79 , CYS A:102 , VAL A:118 , ASN A:119 , ASN A:120 , LEU A:147 , HIS A:175 , ALA A:225 , PRO A:229 , HOH A:2074 , HOH A:2167 , HOH A:2168 , HOH A:2169 , HOH A:2170 , HOH A:2171 , HOH A:2172BINDING SITE FOR RESIDUE NAD A1307
7AC7SOFTWAREGLY C:11 , PHE C:12 , VAL C:13 , ASP C:33 , ILE C:34 , VAL C:35 , TYR C:65 , THR C:77 , SER C:78 , GLY C:79 , CYS C:102 , ASN C:119 , ASN C:120 , GLN C:143 , LEU C:147 , HIS C:175 , ALA C:225 , PRO C:229 , HOH C:2054 , HOH C:2140 , HOH C:2141 , HOH C:2142BINDING SITE FOR RESIDUE NAD C1307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GUY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:120 -Pro A:121
2Asn C:120 -Pro C:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GUY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GUY)

(-) Exons   (0, 0)

(no "Exon" information available for 1GUY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:296
 aligned with MDH_CHLAA | P80040 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
            MDH_CHLAA     1 MRKKISIIGAGFVGSTTAHWLAAKELGDIVLLDFVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTL 306
               SCOP domains d1guya1 A:1-143 Malate dehydrogenase                                                                                                           d1guya2 A:144-306 Malate dehydrogenase                                                                                                                              SCOP domains
               CATH domains 1guyA01 A:1-144 NAD(P)-binding Rossmann-like Domain                                                                                             1guyA02 A:145-305 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee....----------hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eee..ee.hhh.ee.hhh.eee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1guy A   1 MRKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGA----------LIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTL 306
                                    10        20        30        40        50        60        70        80         -|      100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
                                                                                                          80         91                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:300
 aligned with MDH_CHLAA | P80040 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
            MDH_CHLAA     1 MRKKISIIGAGFVGSTTAHWLAAKELGDIVLLDFVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTL 306
               SCOP domains d1guyc1 C:1-143 Malate dehydrogenase                                                                                                           d1guyc2 C:144-306 Malate dehydrogenase                                                                                                                              SCOP domains
               CATH domains 1guyC01 C:1-144 NAD(P)-binding Rossmann-like Domain                                                                                             1guyC02 C:145-305 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee....------.hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eee..ee.hhh.ee.hhh.eee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1guy C   1 MRKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGA------SREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTL 306
                                    10        20        30        40        50        60        70        80      | 90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
                                                                                                          80     87
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GUY)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (MDH_CHLAA | P80040)
molecular function
    GO:0030060    L-malate dehydrogenase activity    Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MDH_CHLAA | P80040: 1ur5 1uxg 1uxh 1uxi 1uxj 1uxk 4cl3

(-) Related Entries Specified in the PDB File

1guz STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
1gv0 STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
1gv1 STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES