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(-) Description

Title :  PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND 4-HYDROXY-1,2,5-THIADIAZOLE-3-CARBOXYLIC ACID
 
Authors :  A. Cameron, J. Read, R. Tranter, V. J. Winter, R. B. Sessions, R. L. Brady A. Easton, H. Kendrick, S. L. Croft, D. Barros, J. L. Lavandera, J. J. Ma F. Risco, S. Garcia-Ochoa, F. J. Gamo, L. Sanz, L. Leon, J. R. Ruiz, R. Ga A. Mallo, F. G. De Las Heras
Date :  20 Apr 04  (Deposition) - 11 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Protein-Ligand Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Cameron, J. Read, R. Tranter, V. J. Winter, R. B. Sessions, R. L. Brady, L. Vivas, A. Easton, H. Kendrick, S. L. Croft, D. Barros, J. L. Lavandera, J. J. Martin, F. Risco, S. Garcia-Ochoa, F. J. Gamo, L. Sanz, L. Leon, J. R. Ruiz, R. Gabarro, A. Mallo, F. G. De Las Heras
Identification And Activity Of A Series Of Azole-Based Compounds With Lactate Dehydrogenase-Directed Anti-Malarial Activity.
J. Biol. Chem. V. 279 31429 2004
PubMed-ID: 15117937  |  Reference-DOI: 10.1074/JBC.M402433200

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LDH
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Synonym: LDH-P

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GBD1Ligand/Ion4-HYDROXY-1,2,5-THIADIAZOLE-3-CARBOXYLIC ACID
2NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GBD4Ligand/Ion4-HYDROXY-1,2,5-THIADIAZOLE-3-CARBOXYLIC ACID
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:27 , GLY A:29 , MET A:30 , ILE A:31 , PHE A:52 , ASP A:53 , ILE A:54 , VAL A:55 , TYR A:85 , THR A:97 , ALA A:98 , GLY A:99 , PHE A:100 , LEU A:112 , VAL A:138 , ASN A:140 , LEU A:163 , LEU A:167 , HIS A:195 , GBD A:401 , HOH A:421 , HOH A:422 , HOH A:424 , HOH A:425 , HOH A:426 , HOH A:427 , HOH A:445 , HOH A:605 , HOH A:608 , HOH A:635BINDING SITE FOR RESIDUE NAI A 416
2AC2SOFTWAREARG A:109 , ASN A:140 , LEU A:167 , ARG A:171 , HIS A:195 , SER A:245 , PRO A:246 , NAI A:416 , HOH A:605BINDING SITE FOR RESIDUE GBD A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T26)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LDH_PLAFD_001 *A73SLDH_PLAFD  ---  ---AA91S
2UniProtVAR_LDH_PLAFD_002 *D96LLDH_PLAFD  ---  ---AD110L
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LDH_PLAFD_001 *A73SLDH_PLAFD  ---  ---AA91S
2UniProtVAR_LDH_PLAFD_002 *D96LLDH_PLAFD  ---  ---AD110L
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T26)

(-) Exons   (0, 0)

(no "Exon" information available for 1T26)

(-) 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:315
 aligned with LDH_PLAFD | Q27743 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:315
                                                                                                                                                                                                                                                                                                                                                   316 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312   | 
           LDH_PLAFD      3 PKAKIVLVGSGMIGGVMATLIVQKNLGDVVLFDIVKNMPHGKALDTSHTNVMAYSNCKVSGSNTYDDLAGADVVIVTAGFTKAPGKSDKEWNRDDLLPLNNKIMIEIGGHIKKNCPNAFIIVVTNPVDVMVQLLHQHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNAHIVGAHGNKMVLLKRYITVGGIPLQEFINNKLISDAELEAIFDRTVNTALEIVNLHASPYVAPAAAIIEMAESYLKDLKKVLICSTLLEGQYGHSDIFGGTPVVLGANGVEQVIELQLNSEEKAKFDEAIAETKRMKALA-    -
               SCOP domains d1t26a1 A:19-163 Lactate dehydrogenase                                                                                                              d1t26a2 A:164-330 Lactate dehydrogenase                                                                                                                                 SCOP domains
               CATH domains 1t26A01 A:19-162 NAD(P)-binding Rossmann-like Domain                                                                                               1t26A02 A:163-329 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            - CATH domains
               Pfam domains --Ldh_1_N-1t26A02 A:21-163                                                                                                                          -Ldh_1_C-1t26A01 A:165-328                                                                                                                                           -- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee...............hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------S----------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1t26 A   19 PKAKIVLVGSGMIGGVMATLIVQKNLGDVVLFDIVKNMPHGKALDTSHTNVMAYSNCKVSGSNTYDDLAGADVVIVTAGFTKAPGKSDKEWNRDDLLPLNNKIMIEIGGHIKKNCPNAFIIVVTNPVDVMVQLLHQHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNAHIVGAHGNKMVLLKRYITVGGIPLQEFINNKLISDAELEAIFDRTVNTALEIVNLHASPYVAPAAAIIEMAESYLKDLKKVLICSTLLEGQYGHSDIFGGTPVVLGANGVEQVIELQLNSEEKAKFDEAIAETKRMKALAH  330
                                    28    ||  39       |50        60        70  ||    79 ||     90       100  |||||106       116       126     ||135       145       155       165       175       185       195       205   ||||211    || 222||     233       243       253       263       273       283|      294    || 305       315       325     
                                         33|          47|                     73A|      81|                103A||||||                       132A|                                                                         209A|||||   216|  223|                                                       283|           299|                             
                                          35           49                      73B       83                 103B|||||                        132B                                                                          209B||||    218   225                                                        285            301                             
                                                                                                             103C||||                                                                                                       209C|||                                                                                                                    
                                                                                                              103D|||                                                                                                        209D||                                                                                                                    
                                                                                                               103E||                                                                                                         210A|                                                                                                                    
                                                                                                                105A|                                                                                                          210B                                                                                                                    
                                                                                                                 105B
   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  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (LDH_PLAFD | Q27743)
molecular function
    GO:0004459    L-lactate dehydrogenase activity    Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LDH_PLAFD | Q27743: 1ceq 1cet 1ldg 1t24 1t25 1t2c 1t2d 1t2e 1u4o 1u4s 1u5a 1u5c 1xiv 2a94 2x8l 4plz

(-) Related Entries Specified in the PDB File

1ldg PFLDH COMPLEXED WITH NADH AND OXAMATE
1t24 PFLDH COMPLEXED WITH NAD+ AND 4-HYDROXY-1,2,5-OXADIAZOLE-3- CARBOXYLIC ACID
1t25 PFLDH COMPLEXED WITH NADH AND 3-HYDROXYISOXAZOLE-4- CARBOXYLIC ACID
1t2c PFLDH COMPLEXED WITH NADH
1t2d PFLDH COMPLEXED WITH NAD+ AND OXALATE
1t2e PFLDH COMPLEXED WITH NAD+ AND 4-HYDROXY-1,2,5-OXADIAZOLE-3- CARBOXYLIC ACID
1t2f HUMAN LDH COMPLEXED WITH NAD+ AND 4-HYDROXY-1,2,5- OXADIAZOLE-3-CARBOXYLIC ACID