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(-) Description

Title :  SOLUTION STRUCTURE OF L. CASEI DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH, 30 STRUCTURES
 
Authors :  V. Polshakov, J. Feeney, B. Birdsall, N. Kovalevskaya
Date :  28 Jun 11  (Deposition) - 21 Dec 11  (Release) - 21 Dec 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
NMR Structure *:  A  (1x)
Keywords :  Oxidoreductase, Dhfr, Positive Cooperativity, Protein-Ligand Interactions (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Feeney, B. Birdsall, N. V. Kovalevskaya, Y. D. Smurnyy, E. M. Navarro Peran, V. I. Polshakov
Nmr Structures Of Apo L. Casei Dihydrofolate Reductase And Its Complexes With Trimethoprim And Nadph: Contributions To Positive Cooperative Binding From Ligand-Induced Refolding, Conformational Changes, And Interligand Hydrophobic Interactions
Biochemistry V. 50 3609 2011
PubMed-ID: 21410224

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    ChainsA
    EC Number1.5.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainNF1
    Expression System Taxid562
    Expression System VectorPMT702
    GeneFOLA, DHFR
    Organism ScientificLACTOBACILLUS CASEI
    Organism Taxid1582

 Structural Features

(-) Chains, Units

  1
NMR Structure (30x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:6 , ILE A:13 , GLY A:14 , LYS A:15 , ASP A:16 , GLY A:17 , HIS A:18 , LEU A:19 , GLY A:42 , ARG A:43 , ARG A:44 , THR A:45 , LEU A:62 , HIS A:64 , HIS A:77 , VAL A:79 , ALA A:97 , GLY A:99 , ALA A:100 , GLN A:101 , ILE A:102 , THR A:126BINDING SITE FOR RESIDUE NDP A 170

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LF1)

(-) Cis Peptide Bonds  (2, 60)

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, 24, 25, 26, 27, 28, 29, 30Arg 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, 24, 25, 26, 27, 28, 29, 30Gly A:98 -Gly A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LF1)

(-) 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 2LF1)

(-) 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 d2lf1a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eee........hhhhhhhhhhhh...eeeeehhhhhh.........eeeee..........eeee.hhhhhhhhhhhh....eeeeehhhhhhhhhhhh.eeeeee........ee........eeeeeeeee...hhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------DHFR_1  PDB: A:12-34   -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2lf1 A   1 TAFLWAQDRDGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQAQGAVVVHDVAAVFAYAKQHPDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVSSRTVEDTNPALTHTYEVWQKKA 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LF1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LF1)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_LACCA | P003811ao8 1bzf 1dis 1diu 1lud 2hm9 2hqp 2l28 3dfr

(-) Related Entries Specified in the PDB File

1lud L.CASEI DHFR-TMP-NADPH
2hm9 L.CASEI DHFR-TMP
2l28 L.CASEI DHFR UNCOMPLEXED