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(-) Description

Title :  SOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIMETHOPRIM AND NADPH, 24 STRUCTURES
 
Authors :  V. I. Polshakov, E. G. Smirnov, B. Birdsall, G. Kelly, J. Feeney
Date :  22 May 02  (Deposition) - 18 Dec 02  (Release) - 28 Dec 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (24x)
NMR Structure *:  A  (1x)
Keywords :  Dhfr, Inhibitor-Enzyme Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. I. Polshakov, E. G. Smirnov, B. Birdsall, G. Kelly, J. Feeney
Nmr-Based Solution Structure Of The Complex Of Lactobacillu Casei Dihydrofolate Reductase With Trimethoprim And Nadph
J. Biomol. Nmr V. 24 67 2002
PubMed-ID: 12449420  |  Reference-DOI: 10.1023/A:1020659713373
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMT702
    Expression System Strain: NF1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOBACILLUS CASEI
    Organism Taxid: 1582

 Structural Features

(-) Chains, Units

  1
NMR Structure (24x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2TRR1Ligand/Ion2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM
NMR Structure * (2, 2)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2TRR1Ligand/Ion2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:5 , ALA A:6 , ILE A:13 , GLY A:14 , LYS A:15 , GLY A:17 , GLY A:42 , ARG A:43 , ARG A:44 , THR A:45 , LEU A:62 , THR A:63 , HIS A:64 , GLN A:65 , ALA A:97 , GLY A:99 , ALA A:100 , GLN A:101 , ILE A:102 , TRR A:170BINDING SITE FOR RESIDUE NDP A 168
2AC2SOFTWARELEU A:4 , TRP A:5 , ALA A:6 , GLY A:17 , LEU A:19 , ASP A:26 , LEU A:27 , PHE A:30 , PHE A:49 , PRO A:50 , ALA A:97 , THR A:116 , NDP A:168BINDING SITE FOR RESIDUE TRR A 170

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 48)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24Arg A:52 -Pro A:53
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24Gly A:98 -Gly A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_LACCA13-35  1A:12-34
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_LACCA13-35  1A:12-34

(-) Exons   (0, 0)

(no "Exon" information available for 1LUD)

(-) Sequences/Alignments

NMR Structure
   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:162
 aligned with DYR_LACCA | P00381 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
            DYR_LACCA     2 TAFLWAQDRDGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQAQGAVVVHDVAAVFAYAKQHPDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVSSRTVEDTNPALTHTYEVWQKKA 163
               SCOP domains d1luda_ A: Dihydrofolate reductase, prokaryotic type                                                                                                               SCOP domains
               CATH domains 1ludA00 A:1-162 Dihydrofolate Reductase, subunit A                                                                                                                 CATH domains
               Pfam domains DHFR_1-1ludA01 A:1-160                                                                                                                                          -- Pfam domains
         Sec.struct. author .eeeeee...............hhhhhhhhhhhh...eeeeehhhhhhh........eeeee...........eee.hhhhhhhhhhhh....eeeeehhhhhhhh.....eeeeeee.............hhh.eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------DHFR_1  PDB: A:12-34   -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lud A   1 TAFLWAQDRDGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQAQGAVVVHDVAAVFAYAKQHPDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVSSRTVEDTNPALTHTYEVWQKKA 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
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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  (1, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: DHFred (95)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (DYR_LACCA | P00381)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    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.
biological process
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0031427    response to methotrexate    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methotrexate stimulus. Methotrexate is 4-amino-10-methylformic acid, a folic acid analogue that is a potent competitive inhibitor of dihydrofolate reductase.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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  1.5.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_LACCA | P00381: 1ao8 1bzf 1dis 1diu 2hm9 2hqp 2l28 2lf1 3dfr

(-) Related Entries Specified in the PDB File

1ao8 1AO8 CONTAINS THE SAME PROTEIN COMPLEXED WITH METHOTREXATE
1bzf 1BZF CONTAINS THE SAME PROTEIN COMPLEXED WITH THE NEW LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE
3dfr 3DFR CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH NADPH AND METHOTREXATE