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(-) Description

Title :  CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF ESCHERICHIA COLI MALATE DEHYDROGENASE, CITRATE AND NAD AT 1.9 ANGSTROMS RESOLUTION
 
Authors :  M. D. Hall, L. J. Banaszak
Date :  25 Mar 93  (Deposition) - 31 Oct 93  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase(Nad(A)-Choh(D)) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. D. Hall, L. J. Banaszak
Crystal Structure Of A Ternary Complex Of Escherichia Coli Malate Dehydrogenase Citrate And Nad At 1. 9 A Resolution.
J. Mol. Biol. V. 232 213 1993
PubMed-ID: 8331658  |  Reference-DOI: 10.1006/JMBI.1993.1377

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    ChainsA
    EC Number1.1.1.37
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 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
1CIT1Ligand/IonCITRIC ACID
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:12 , ARG A:81 , ARG A:87 , ASN A:119 , ARG A:153 , HIS A:177 , GLY A:210 , ALA A:223 , NAD A:314 , HOH A:349 , HOH A:350 , HOH A:398BINDING SITE FOR RESIDUE CIT A 313
2AC2SOFTWAREALA A:9 , GLY A:10 , GLY A:11 , ILE A:12 , TYR A:33 , ASP A:34 , ILE A:35 , SER A:76 , ALA A:77 , GLY A:78 , VAL A:79 , ARG A:80 , ASN A:94 , ILE A:117 , THR A:118 , ASN A:119 , VAL A:121 , VAL A:146 , HIS A:177 , THR A:224 , MET A:227 , CIT A:313 , HOH A:316 , HOH A:332 , HOH A:342 , HOH A:398 , HOH A:399BINDING SITE FOR RESIDUE NAD A 314
3ACTUNKNOWNARG A:81 , ARG A:87 , ASP A:150 , ARG A:153 , HIS A:177NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:119 -Pro A:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_MDH_ECOLI_001 *D71NMDH_ECOLI  ---  ---AD71N
02UniProtVAR_MDH_ECOLI_002 *A106SMDH_ECOLI  ---  ---AA106S
03UniProtVAR_MDH_ECOLI_003 *A209PMDH_ECOLI  ---  ---AA209P
04UniProtVAR_MDH_ECOLI_004 *A218RMDH_ECOLI  ---  ---AA218R
05UniProtVAR_MDH_ECOLI_005 *A232TMDH_ECOLI  ---  ---AA232T
06UniProtVAR_MDH_ECOLI_006 *V249IMDH_ECOLI  ---  ---AV249I
07UniProtVAR_MDH_ECOLI_007 *Q289KMDH_ECOLI  ---  ---AQ289K
08UniProtVAR_MDH_ECOLI_008 *N290SMDH_ECOLI  ---  ---AN290S
09UniProtVAR_MDH_ECOLI_009 *A291SMDH_ECOLI  ---  ---AA291S
10UniProtVAR_MDH_ECOLI_010 *G294AMDH_ECOLI  ---  ---AG294A
11UniProtVAR_MDH_ECOLI_011 *D297NMDH_ECOLI  ---  ---AD297N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (11, 22)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_MDH_ECOLI_001 *D71NMDH_ECOLI  ---  ---AD71N
02UniProtVAR_MDH_ECOLI_002 *A106SMDH_ECOLI  ---  ---AA106S
03UniProtVAR_MDH_ECOLI_003 *A209PMDH_ECOLI  ---  ---AA209P
04UniProtVAR_MDH_ECOLI_004 *A218RMDH_ECOLI  ---  ---AA218R
05UniProtVAR_MDH_ECOLI_005 *A232TMDH_ECOLI  ---  ---AA232T
06UniProtVAR_MDH_ECOLI_006 *V249IMDH_ECOLI  ---  ---AV249I
07UniProtVAR_MDH_ECOLI_007 *Q289KMDH_ECOLI  ---  ---AQ289K
08UniProtVAR_MDH_ECOLI_008 *N290SMDH_ECOLI  ---  ---AN290S
09UniProtVAR_MDH_ECOLI_009 *A291SMDH_ECOLI  ---  ---AA291S
10UniProtVAR_MDH_ECOLI_010 *G294AMDH_ECOLI  ---  ---AG294A
11UniProtVAR_MDH_ECOLI_011 *D297NMDH_ECOLI  ---  ---AD297N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MDHPS00068 Malate dehydrogenase active site signature.MDH_ECOLI146-158  1A:146-158
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MDHPS00068 Malate dehydrogenase active site signature.MDH_ECOLI146-158  2A:146-158

(-) Exons   (0, 0)

(no "Exon" information available for 1EMD)

(-) 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:312
 aligned with MDH_ECOLI | P61889 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:312
                                    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       310  
            MDH_ECOLI     1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
               SCOP domains d1emda1 A:1-145 Malate dehydrogenase                                                                                                             d1emda2 A:146-312 Malate dehydrogenase                                                                                                                                  SCOP domains
               CATH domains 1emdA01 A:1-146 NAD(P)-binding Rossmann-like Domain                                                                                               1emdA02 A:147-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) eeeeeee..hhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh...eeeeeee...hhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh........----hhhhhhhhhhhhhhhh.........eeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.......eeeeeee..eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------eeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------N----------------------------------S------------------------------------------------------------------------------------------------------P--------R-------------T----------------I---------------------------------------KSS--A--N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1emd A   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVRRKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGQEFVNK 312
                                    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       310  

   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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (MDH_ECOLI | P61889)
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:0016615    malate dehydrogenase activity    Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
    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:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    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:0006113    fermentation    The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0006108    malate metabolic process    The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDH_ECOLI | P618891cme 1ib6 1ie3 2cmd 2pwz 3hhp 5kka

(-) Related Entries Specified in the PDB File

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