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(-) Description

Title :  NOVEL CRYSTALLIZATION CONDITIONS FOR TANDEM VARIANT R67 DHFR YIELDS WILD-TYPE CRYSTAL STRUCTURE
 
Authors :  B. J. Yachnin, A. M. Berghuis
Date :  13 Jun 11  (Deposition) - 02 Nov 11  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase, Dihydrofolate Reductase, Antibiotic Resistance, In Situ Proteolysis, Type Ii Dhfr, Sh3, Reductase, Dhf And Nadph- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Yachnin, D. Y. Colin, J. P. Volpato, M. Ebert, J. N. Pelletier, A. M. Berghuis
Novel Crystallization Conditions For Tandem Variant R67 Dhf Yield A Wild-Type Crystal Structure.
Acta Crystallogr. , Sect. F V. 67 1316 2011
PubMed-ID: 22102224  |  Reference-DOI: 10.1107/S1744309111030417

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE TYPE 2
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-32-DERIVED
    Expression System Strain: BL21(PREP4)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 21-78
    Gene: DFRB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    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, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MRD12Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:22 , ARG A:76 , HOH A:109BINDING SITE FOR RESIDUE MRD A 400
2AC2SOFTWAREALA A:22 , PHE A:24 , MET A:26 , TRP A:45BINDING SITE FOR RESIDUE MRD A 401
3AC3SOFTWAREGLY A:35 , LEU A:50BINDING SITE FOR RESIDUE MRD A 402

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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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 d3sfma_ A: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee......eeeeeeee.......eeeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3sfm A 21 DATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN 78
                                    30        40        50        60        70
   Legend:   → Mismatch (orange background)
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SFM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SFM)

(-) 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

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UniProtKB/Swiss-Prot
        DYR21_ECOLX | P00383: 1vie 1vif 2gqv 2p4t 2rh2 2rk1 2rk2

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