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(-) Description

Title :  CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION
 
Authors :  A. D. M. Chapman, A. Cortes, T. R. Dafforn, A. R. Clarke, R. L. Brady
Date :  08 Oct 98  (Deposition) - 18 May 99  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, (Nad(A)-Choh(D)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Chapman, A. Cortes, T. R. Dafforn, A. R. Clarke, R. L. Brady
Structural Basis Of Substrate Specificity In Malate Dehydrogenases: Crystal Structure Of A Ternary Complex Of Porcine Cytoplasmic Malate Dehydrogenase, Alpha-Ketomalonat And Tetrahydonad.
J. Mol. Biol. V. 285 703 1999
PubMed-ID: 10075524  |  Reference-DOI: 10.1006/JMBI.1998.2357
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Cellular Location: CYTOPLASM
    Chains: A, B
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organ: HEART
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Tissue: MUSCLE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MAK2Ligand/IonALPHA-KETOMALONIC ACID
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , ALA A:12 , GLY A:13 , GLN A:14 , ILE A:15 , ASP A:41 , VAL A:86 , GLY A:87 , SER A:88 , MET A:89 , PRO A:90 , ILE A:107 , VAL A:128 , GLY A:129 , ASN A:130 , LEU A:154 , HIS A:186 , SER A:240 , SER A:241 , ALA A:245 , MAK A:335 , HOH A:412 , HOH A:465 , HOH A:518 , GLY B:301BINDING SITE FOR RESIDUE NAD A 334
2AC2SOFTWAREARG A:91 , ARG A:97 , ASN A:130 , LEU A:157 , ARG A:161 , HIS A:186 , ILE A:234 , SER A:241 , NAD A:334 , HOH A:365BINDING SITE FOR RESIDUE MAK A 335
3AC3SOFTWAREGLY B:10 , GLY B:13 , GLN B:14 , ILE B:15 , ASP B:41 , ILE B:42 , VAL B:86 , GLY B:87 , SER B:88 , ILE B:107 , GLN B:111 , VAL B:128 , GLY B:129 , ASN B:130 , LEU B:154 , LEU B:157 , HIS B:186 , SER B:240 , MAK B:335 , HOH B:359 , HOH B:383 , HOH B:421BINDING SITE FOR RESIDUE NAD B 334
4AC4SOFTWARELEU B:157 , ASP B:158 , ARG B:161 , HIS B:186 , GLY B:230 , NAD B:334BINDING SITE FOR RESIDUE MAK B 335

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:136 -A:153
2B:136 -B:153

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5MDH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MDH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MDH)

(-) Exons   (0, 0)

(no "Exon" information available for 5MDH)

(-) Sequences/Alignments

Asymmetric/Biological 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d5mdha1 A:1-154 Malate dehydrogenase                                                                                                                      d5mdha2 A:155-333 Malate dehydrogenase                                                                                                                                              SCOP domains
               CATH domains 5mdhA01 A:1-153 NAD(P)-binding Rossmann-like Domain                                                                                                      5mdhA02 A:154-333 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhh.hhhhh..........eeeeee..hhhhhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...............hhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....hhheee..hhhhhhhhhhhhhhh...hhh....eee.......eee....eee....eeehhhhh..hhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......eeeeee............eeeeeeeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mdh A   1 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA 333
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Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d5mdhb1 B:1-154 Malate dehydrogenase                                                                                                                      d5mdhb2 B:155-333 Malate dehydrogenase                                                                                                                                              SCOP domains
               CATH domains 5mdhB01 B:1-153 NAD(P)-binding Rossmann-like Domain                                                                                                      5mdhB02 B:154-333 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhh..........eeeeee..hhhhhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...............hhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhh......hhheee..hhhhhhhhhhhhhhh...hhh....eee.......eee..............hhhhh..hhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......eeeeee............eeeeeeeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mdh B   1 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA 333
                                    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       320       330
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MDH)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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