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(-) Description

Title :  2.8 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH ETHENO-NAD
 
Authors :  A. Irimia, D. Madern, G. Zaccai, F. M. Vellieux, A. Karshikoff, G. Tibbelin, R. Ladenstein, T. Lien, N. K. Birkeland
Date :  14 Dec 09  (Deposition) - 22 Dec 09  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Hyperthermophilic, Tricarboxylic Acid Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Irimia, F. M. D. Vellieux, D. Madern, G. Zaccai, A. Karshikoff, G. Tibbelin, R. Ladenstein, T. Lien, N. K. Birkeland
The 2. 9A Resolution Crystal Structure Of Malate Dehydrogenase From Archaeoglobus Fulgidus: Mechanisms Of Oligomerisation And Thermal Stabilisation.
J. Mol. Biol. V. 335 343 2004
PubMed-ID: 14659762  |  Reference-DOI: 10.1016/J.JMB.2003.10.054
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSJS1240
    Expression System Strain: ONE SHOT
    Expression System Taxid: 562
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS DSM 4304
    Organism Taxid: 224325

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ENA1Ligand/IonETHENO-NAD
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ENA2Ligand/IonETHENO-NAD
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , ARG A:31 , VAL A:32 , ASP A:53 , ILE A:54 , LEU A:58 , TYR A:85 , THR A:97 , ALA A:98 , GLY A:99 , ILE A:119 , VAL A:138 , ASN A:140 , MET A:142 , MET A:163 , LEU A:167 , HIS A:195 , THR A:246 , PRO A:250 , SO4 A:2000 , HOH A:2029 , HOH A:2030BINDING SITE FOR RESIDUE ENA A1000
2AC2SOFTWAREASN A:140 , LEU A:167 , ARG A:171 , HIS A:195 , ALA A:236 , THR A:246 , ENA A:1000BINDING SITE FOR RESIDUE SO4 A2000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X0J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:140 -Pro A:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X0J)

(-) Exons   (0, 0)

(no "Exon" information available for 2X0J)

(-) 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:294
 aligned with MDH_ARCFU | O08349 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:294
                                    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    
           MDH_ARCFU      1 MKLGFVGAGRVGSTSAFTCLLNLDVDEIALVDIAEDLAVGEAMDLAHAAAGIDKYPKIVGGADYSLLKGSEIIVVTAGLARKPGMTRLDLAHKNAGIIKDIAKKIVENAPESKILVVTNPMDVMTYIMWKESGKPRNEVFGMGNQLDSQRLKERLYNAGARNIRRAWIIGEHGDSMFVAKSLADFDGEVDWEAVENDVRFVAAEVIKRKGATIFGPAVAIYRMVKAVVEDTGEIIPTSMILQGEYGIENVAVGVPAKLGKNGAEVADIKLSDEEIEKLRNSAKILRERLEELGY  294
               SCOP domains d2x0ja1 A:22-163 Malate dehydrogenase                                                                                                         d2x0ja2 A:164-331 Lactate dehydrogenase                                                                                                                  SCOP domains
               CATH domains 2x0jA01 A:22-163 NAD(P)-binding Rossmann-like Domain                                                                                          2x0jA02 A:164-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                              CATH domains
               Pfam domains Ldh_1_N-2x0jA02 A:22-163                                                                                                                      --Ldh_1_C-2x0jA01 A:166-330                                                                                                                            - Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhh..eee....ee.......ee.hhhh.ee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.eeeeeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2x0j A   22 MKLGFVGAGRVGSTSAFTCLLNLDVDEIALVDIAEDLAVGEAMDLAHAAAGIDKYPKIVGGADYSLLKGSEIIVVTAGLARKPGMTRLDLAHKNAGIIKDIAKKIVENAPESKILVVTNPMDVMTYIMWKESGKPRNEVFGMGNQLDSQRLKERLYNAGARNIRRAWIIGEHGDSMFVAKSLADFDGEVDWEAVENDVRFVAAEVIKRKGATIFGPAVAIYRMVKAVVEDTGEIIPTSMILQGEYGIENVAVGVPAKLGKNGAEVADIKLSDEEIEKLRNSAKILRERLEELGY  331
                                    31        41        51        61       71A|       80|||     91       101 ||    112       122      132A|      141       151       161       171       182||||   193       203     ||224       234       244       254       264       274     ||285       295  ||   307       317       327    
                                                                           71A|        81||                103|                       132A|                                             180|||||                   209||||                                                     280|             298|                              
                                                                            71B        84A|                 105                        132B                                              182||||                    212|||                                                      282              301                              
                                                                                        84B                                                                                               183|||                     219||                                                                                                        
                                                                                                                                                                                           186||                      220|                                                                                                        
                                                                                                                                                                                           187A|                       224                                                                                                        
                                                                                                                                                                                            187B
   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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (MDH_ARCFU | O08349)
molecular function
    GO:0004459    L-lactate dehydrogenase activity    Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + NADH + H+.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

2x0i 2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH NADH