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(-) Description

Title :  STABILIZATION OF A TETRAMERIC MALATE DEHYDROGENASE BY INTRODUCTION OF A DISULFIDE BRIDGE AT THE DIMER/DIMER INTERFACE
 
Authors :  A. Bjork, B. Dalhus, D. Mantzilas, V. G. H. Eijsink, R. Sirevag
Date :  27 Oct 03  (Deposition) - 05 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Oxidoreductase, Tricarboxylic Acid Cycle, Malate Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bjork, B. Dalhus, D. Mantzilas, V. G. H. Eijsink, R. Sirevag
Stabilization Of A Tetrameric Malate Dehydrogenase By Introduction Of A Disulfide Bridge At The Dimer-Dimer Interface
J. Mol. Biol. V. 334 811 2003
PubMed-ID: 14636605  |  Reference-DOI: 10.1016/J.JMB.2003.10.006

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, C
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Mutation: YES
    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  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CD6Ligand/IonCADMIUM ION
2CL1Ligand/IonCHLORIDE ION
3NA2Ligand/IonSODIUM ION
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
4NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:178 , CL A:1312 , HOH A:2156 , HOH A:2157BINDING SITE FOR RESIDUE CD A1309
02AC2SOFTWAREGLU A:165 , HOH C:2203 , HOH C:2211BINDING SITE FOR RESIDUE CD A1310
03AC3SOFTWAREASP A:200 , ASP A:243 , GLU A:277 , HOH A:2238BINDING SITE FOR RESIDUE CD A1311
04AC4SOFTWAREASP A:123 , ALA A:124 , CD A:1309BINDING SITE FOR RESIDUE CL A1312
05AC5SOFTWAREHIS A:19BINDING SITE FOR RESIDUE NA A1313
06AC6SOFTWAREGLU C:178 , HOH C:2083 , HOH C:2113 , HOH C:2115BINDING SITE FOR RESIDUE CD C1310
07AC7SOFTWAREHOH A:2212 , GLU C:165BINDING SITE FOR RESIDUE CD C1311
08AC8SOFTWAREGLU A:159 , HOH A:2139 , GLU C:159 , HOH C:2140BINDING SITE FOR RESIDUE CD C1312
09AC9SOFTWAREHIS C:19BINDING SITE FOR RESIDUE NA C1313
10BC1SOFTWAREGLY A:9 , GLY A:11 , PHE A:12 , VAL A:13 , ASP A:33 , ILE A:34 , VAL A:35 , TYR A:65 , THR A:77 , SER A:78 , GLY A:79 , VAL A:118 , ASN A:119 , ASN A:120 , LEU A:147 , HIS A:175 , ALA A:225 , PRO A:229 , HOH A:2277 , HOH A:2278 , HOH A:2279 , HOH A:2280 , HOH A:2281 , HOH A:2282BINDING SITE FOR RESIDUE NAD A1308
11BC2SOFTWAREGLY C:9 , GLY 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 , ALA C:80 , CYS C:102 , VAL C:118 , ASN C:120 , LEU C:147 , HIS C:175 , PRO C:229 , HOH C:2197 , HOH C:2262 , HOH C:2263 , HOH C:2264 , HOH C:2265BINDING SITE FOR RESIDUE NAD C1309

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:187 -C:187
2A:187 -C:187

(-) 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 1UR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UR5)

(-) Exons   (0, 0)

(no "Exon" information available for 1UR5)

(-) 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:299
 aligned with MDH_CHLAA | P80040 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       
            MDH_CHLAA     2 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDFVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKS 308
               SCOP domains d1ur5a1 A:2-143 Malate dehydrogenase                                                                                                          d1ur5a2 A:144-308 Malate dehydrogenase                                                                                                                                SCOP domains
               CATH domains 1ur5A01 A:2-144 NAD(P)-binding Rossmann-like Domain                                                                                            1ur5A02 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....--------hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eee..ee.hhh.ee.hhh.eee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur5 A   2 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGA--------EDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSCISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKS 308
                                    11        21        31        41        51        61        71        |-       |91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       
                                                                                                         80       89                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:301
 aligned with MDH_CHLAA | P80040 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
            MDH_CHLAA     2 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDFVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKSL 309
               SCOP domains d1ur5c1 C:2-143 Malate dehydrogenase                                                                                                          d1ur5c2 C:144-309 Malate dehydrogenase                                                                                                                                 SCOP domains
               CATH domains 1ur5C01 C:2-144 NAD(P)-binding Rossmann-like Domain                                                                                            1ur5C02 C:145-305 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                      ---- CATH domains
           Pfam domains (1) -Ldh_1_N-1ur5C03 C:3-143                                                                                                                      -Ldh_1_C-1ur5C01 C:145-309                                                                                                                                             Pfam domains (1)
           Pfam domains (2) -Ldh_1_N-1ur5C04 C:3-143                                                                                                                      -Ldh_1_C-1ur5C02 C:145-309                                                                                                                                             Pfam domains (2)
         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.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur5 C   2 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGA-------REDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSCISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKSL 309
                                    11        21        31        41        51        61        71        |-      | 91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
                                                                                                         80      88
   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  (2, 4)

Asymmetric Unit
(-)
Clan: LDH_C (56)
(-)
Clan: NADP_Rossmann (1239)

(-) 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: 1guy 1uxg 1uxh 1uxi 1uxj 1uxk 4cl3

(-) Related Entries Specified in the PDB File

1guy STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES