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(-) Description

Title :  CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS
 
Authors :  P. D. Carr, A. R. Ashton, D. Verger, D. L. Ollis
Date :  01 Apr 99  (Deposition) - 05 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Chloroplast, Light Activated, Nadp-Dependent, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Carr, D. Verger, A. R. Ashton, D. L. Ollis
Chloroplast Nadp-Malate Dehydrogenase: Structural Basis Of Light-Dependent Regulation Of Activity By Thiol Oxidation And Reduction.
Structure Fold. Des. V. 7 461 1999
PubMed-ID: 10196131  |  Reference-DOI: 10.1016/S0969-2126(99)80058-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADP-MALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.82
    Organ: LEAF
    Organelle: CHLOROPLAST
    Organism Scientific: FLAVERIA BIDENTIS
    Organism Taxid: 4224
    Other Details: DARKENED LEAVES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:49 , ALA A:50 , ALA A:51 , GLY A:52 , MET A:53 , ILE A:54 , GLY A:80 , SER A:81 , SER A:84 , ALA A:127 , GLN A:150 , VAL A:167 , GLY A:168 , ASN A:169 , LEU A:193 , HIS A:225 , THR A:280 , MET A:380 , GLU A:384 , MET A:385 , HOH A:387 , HOH A:393 , HOH A:394 , HOH A:399 , HOH A:431 , HOH A:440 , HOH A:533BINDING SITE FOR RESIDUE NAP A 386

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:20 -A:25
2A:361 -A:373

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:169 -Pro A:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CIV)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MDHPS00068 Malate dehydrogenase active site signature.MDHP_FLABI261-273  1A:193-205
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MDHPS00068 Malate dehydrogenase active site signature.MDHP_FLABI261-273  2A:193-205

(-) Exons   (0, 0)

(no "Exon" information available for 1CIV)

(-) 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:374
 aligned with MDHP_FLABI | P46489 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:374
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449    
           MDHP_FLABI    80 LPAKQKPECFGVFCLTYDLKAEEETKSWKKIINVAVSGAAGMISNHLLFKLASGEVFGPDQPISLKLLGSERSFAALEGVAMELEDSLYPLLRQVSIGIDPYEIFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNAVASPNVKVMVVGNPCNTNALICLKNAPNIPPKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIHGIPVTEVIRDRKWLEDEFTNMVQTRGGVLIKKWGRSSAASTAVSIVDAIRSLVTPTPEGDWFSTGVYTNGNPYGIAEDIVFSMPCRSKGDGDYEFVKDVIFDDYLSKKIKKSEDELLAEKKCVAHLTGEGIAVCDLPEDTMLPGEM 453
               SCOP domains d1civa1 A:12-193 Malate dehydrogenase                                                                                                                                                 d1civa2 A:194-385 Malate dehydrogenase                                                                                                                                                           SCOP domains
               CATH domains ----------------------------1civA01 A:40-192 NAD(P)-binding Rossmann-like Domain                                                                                                     1civA02 A:193-367 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                    ------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eeeeee....hhhhhhhhhhh..........eeeeee..hhhhhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....hhheee..hhhhhhhhhhhhhhh..........eee.......eee..........hhh....hhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh........eeeeee............eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MDH          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1civ A  12 LPAKQKPECFGVFCLTYDLKAEEETKSWKKIINVAVSGAAGMISNHLLFKLASGEVFGPDQPISLKLLGSERSFAALEGVAMELEDSLYPLLRQVSIGIDPYEIFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNAVASPNVKVMVVGNPCNTNALICLKNAPNIPPKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIHGIPVTEVIRDRKWLEDEFTNMVQTRGGVLIKKWGRSSAASTAVSIVDAIRSLVTPTPEGDWFSTGVYTNGNPYGIAEDIVFSMPCRSKGDGDYEFVKDVIFDDYLSKKIKKSEDELLAEKKCVAHLTGEGIAVCDLPEDTMLPGEM 385
                                    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       311       321       331       341       351       361       371       381
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  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  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (MDHP_FLABI | P46489)
molecular function
    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:0046554    malate dehydrogenase (NADP+) activity    Catalysis of the reaction: (S)-malate + NADP+ = oxaloacetate + NADPH + H+.
    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: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: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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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