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(-) Description

Title :  DHFR R-67 COMPLEXED WITH NADP
 
Authors :  J. M. Krahn, R. E. London
Date :  16 Oct 07  (Deposition) - 03 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase, Nadp, Asymmetric Ligand Binding, Antibiotic Resistance, Methotrexate Resistance, One-Carbon Metabolism, Trimethoprim Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Krahn, M. R. Jackson, E. F. Derose, E. E. Howell, R. E. London
Crystal Structure Of A Type Ii Dihydrofolate Reductase Catalytic Ternary Complex.
Biochemistry V. 46 14878 2007
PubMed-ID: 18052202  |  Reference-DOI: 10.1021/BI701532R

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE TYPE 2
    Chains: A
    EC Number: 1.5.1.3
    Organism Scientific: ESCHERICHIA COLI
    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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1MRD12Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:32 , SER A:34 , GLY A:35 , ALA A:36 , LEU A:50 , GLY A:64 , SER A:65 , GLN A:67 , ILE A:68 , TYR A:69 , PRO A:70 , ALA A:72 , ALA A:73 , HOH A:503 , HOH A:504 , HOH A:506 , HOH A:507 , HOH A:508 , HOH A:509 , HOH A:534 , HOH A:543 , HOH A:546 , HOH A:558 , HOH A:560 , HOH A:565 , HOH A:567 , HOH A:568 , HOH A:576 , HOH A:577 , HOH A:579 , HOH A:582 , HOH A:583 , HOH A:586BINDING SITE FOR RESIDUE NAP A 1
2AC2SOFTWAREALA A:22 , GLY A:25 , ILE A:77 , ASN A:78BINDING SITE FOR RESIDUE MRD A 500
3AC3SOFTWAREGLY A:35 , LEU A:50 , HOH A:574BINDING SITE FOR RESIDUE MRD A 501
4AC4SOFTWAREPHE A:24 , GLY A:25 , TRP A:45 , HOH A:559BINDING SITE FOR RESIDUE MRD A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RK2)

(-) Exons   (0, 0)

(no "Exon" information available for 2RK2)

(-) 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: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 d2rk2a_ A: automated matches                               SCOP domains
               CATH domains 2rk2A00 A:21-78  [code=2.30.30.60, no name defined]        CATH domains
               Pfam domains DHFR_2-2rk2A01 A:21-78                                     Pfam domains
         Sec.struct. author ........eeee......eeeeeeee.......eeeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2rk2 A 21 NATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN 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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  DYR21_ECOLX | P00383
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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
        DYR21_ECOLX | P00383: 1vie 1vif 2gqv 2p4t 2rh2 2rk1 3sfm

(-) Related Entries Specified in the PDB File

2p4t A MUTANT FORM OF THE SAME PROTEIN (Q67H) COMPLEXED WITH NADP. THE MUTANT HAS A HIGHER AFFINITY FOR NADP, BUT APPEARS TO BIND DIFFERENTLY.
2rh2 HIGH RESOLUTION STRUCTURE OF THE SAME PROTEIN WITH NO LIGANDS, USED AS A STARTING MODEL FOR THIS STRUCTURE.