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(-) Description

Title :  STRUCTURE OF THE Q67H MUTANT OF R67 DIHYDROFOLATE REDUCTASE-NADP+ COMPLEX REVEALS A NOVEL COFACTOR BINDING MODE
 
Authors :  N. Divya, E. Grifith, N. Narayana
Date :  13 Mar 07  (Deposition) - 05 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Bacterial Infections, Crystal Structure, Folate Metabolism, Nadp+, R67 Dhfr, Symmetric Binding, Trimethoprim-Resistance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Divya, E. Grifith, N. Narayana
Structure Of The Q67H Mutant Of R67 Dihydrofolate Reductase-Nadp+ Complex Reveals A Novel Cofactor Binding Mode.
Protein Sci. V. 16 1063 2007
PubMed-ID: 17473013  |  Reference-DOI: 10.1110/PS.062740907
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE TYPE 2
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1
    Synonym: DIHYDROFOLATE REDUCTASE TYPE II

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): 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, 4)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:32 , ALA A:36 , VAL A:66 , HIS A:67 , ILE A:68 , TYR A:69 , HOH A:144 , HOH A:145 , HOH A:146 , HOH A:147 , HOH A:149 , HOH A:151 , HOH A:152BINDING SITE FOR RESIDUE NAP A 157

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P4T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P4T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2P4T)

(-) 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    
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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:58
 aligned with DYR21_ECOLX | P00383 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:58
                                    30        40        50        60        70        
           DYR21_ECOLX   21 NATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN 78
               SCOP domains d2p4ta_ A: automated matches                               SCOP domains
               CATH domains 2p4tA00 A:21-78  [code=2.30.30.60, no name defined]        CATH domains
               Pfam domains DHFR_2-2p4tA01 A:21-78                                     Pfam domains
         Sec.struct. author ........eeee......eeeeeeee.......eeeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2p4t A 21 NATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVHIYPVAALERIN 78
                                    30        40        50        60        70
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHFR_2] (6)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DYR21_ECOLX | P00383)
molecular function
    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: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:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    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
        DYR21_ECOLX | P00383: 1vie 1vif 2gqv 2rh2 2rk1 2rk2 3sfm

(-) Related Entries Specified in the PDB File

1vie THE WILD TYPE STRUCTURE AT 1.7 A RESOLUTION
1vif THE WILD TYPE PROTEIN STRUCTURE COMPLEXED WITH FOLATE
2gqv THE WILD TYPE PROTEIN STRUCTURE AT 1.1 A RESOLUTION