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(-) Description

Title :  STRUCTURAL AND KINETIC DATA FOR ANTIFOLATE INTERACTIONS AGAINST PNEUMOCYSTIS JIROVECII, PNEUMOCYSTIS CARINII AND HUMAN DIHYDROFOLATE REDUCTASE AND THIER ACTIVE SITE MUTANTS
 
Authors :  V. Cody
Date :  05 Aug 10  (Deposition) - 03 Aug 11  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Hdhfr Inhibitor Complexes, Oxidoreductase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Cody, J. Pace, S. F. Queener, O. O. Adair, A. Gangjee
Kinetic And Structural Analysis For Potent Antifolate Inhibition Of Pneumocystis Jirovecii, Pneumocystis Carinii, And Human Dihydrofolate Reductases And Their Active-Site Variants.
Antimicrob. Agents Chemother. V. 57 2669 2013
PubMed-ID: 23545530  |  Reference-DOI: 10.1128/AAC.00172-13

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    ChainsA
    EC Number1.5.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDS5
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentHUMAN DIHYDROFOLATE REDUCTASE
    GeneDHFR, DHFRP1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1OAG1Ligand/Ion6-{[(2,5-DICHLOROPHENYL)AMINO]METHYL}PYRIDO[2,3-D]PYRIMIDINE-2,4-DIAMINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:7 , VAL A:8 , ALA A:9 , GLU A:30 , PHE A:31 , PHE A:34 , SER A:59 , PRO A:61 , THR A:136 , HOH A:276BINDING SITE FOR RESIDUE OAG A 187
2AC2SOFTWAREGLY A:53 , LYS A:54 , LYS A:55 , THR A:56 , GLY A:117BINDING SITE FOR RESIDUE SO4 A 188
3AC3SOFTWARELYS A:54 , SER A:76 , ARG A:77 , GLU A:78 , HOH A:215BINDING SITE FOR RESIDUE SO4 A 189
4AC4SOFTWAREGLU A:143 , VAL A:165 , LEU A:166 , SER A:167BINDING SITE FOR RESIDUE SO4 A 190
5AC5SOFTWARELYS A:63BINDING SITE FOR RESIDUE SO4 A 191
6AC6SOFTWAREPRO A:61 , GLU A:62 , ARG A:65 , LYS A:157BINDING SITE FOR RESIDUE SO4 A 192

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OAF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:65 -Pro A:66
2Gly A:116 -Gly A:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065818L80FDYR_HUMANDisease (DHFRD)387906619AL79F
2UniProtVAR_065819D153VDYR_HUMANDisease (DHFRD)121913223AD152V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_HUMAN4-185  1A:3-184
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_HUMAN16-39  1A:15-38

(-) Exons   (0, 0)

(no "Exon" information available for 3OAF)

(-) Sequences/Alignments

Asymmetric/Biological 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:186
 aligned with DYR_HUMAN | P00374 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
            DYR_HUMAN     2 VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND 187
               SCOP domains d3oafa_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....eee.........hhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh....eeeeee............eee.hhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhh...eeeeeeeee.......ee.........ee...........eee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------F------------------------------------------------------------------------V---------------------------------- SAPs(SNPs)
                PROSITE (1) --DHFR_2  PDB: A:3-184 UniProt: 4-185                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) --------------DHFR_1  PDB: A:15-38    ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oaf A   1 VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFSRMTTTSSVEGKQNLVIMGKKTWFSIPEKFRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DYR_HUMAN | P00374)
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:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0033560    folate reductase activity    Catalysis of the reaction: 7,8-dihydrofolate + NADP+ = folate + NADPH + H+.
    GO:0005542    folic acid binding    Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0051870    methotrexate binding    Interacting selectively and non-covalently with methotrexate, an antineoplastic antimetabolite with immunosuppressant properties. It is an inhibitor of tetrahydrofolate reductase and prevents the formation of tetrahydrofolate, necessary for synthesis of thymidylate, an essential component of DNA.
    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:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0031103    axon regeneration    The regrowth of axons following their loss or damage.
    GO:0046452    dihydrofolate metabolic process    The chemical reactions and pathways involving dihydrofolate, the dihydroxylated derivative of folate.
    GO:0046655    folic acid metabolic process    The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    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:0051000    positive regulation of nitric-oxide synthase activity    Any process that activates or increases the activity of the enzyme nitric-oxide synthase.
    GO:2000121    regulation of removal of superoxide radicals    Any process that modulates the frequency, rate or extent of removal of superoxide radicals.
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    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:0006729    tetrahydrobiopterin biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.
    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.
    GO:0046653    tetrahydrofolate metabolic process    The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_HUMAN | P003741boz 1dhf 1dlr 1dls 1drf 1hfp 1hfq 1hfr 1kms 1kmv 1mvs 1mvt 1ohj 1ohk 1pd8 1pd9 1pdb 1s3u 1s3v 1s3w 1u71 1u72 1yho 2c2s 2c2t 2dhf 2w3a 2w3b 2w3m 3eig 3f8y 3f8z 3f91 3fs6 3ghc 3ghv 3ghw 3gi2 3gyf 3l3r 3n0h 3ntz 3nu0 3nxo 3nxr 3nxt 3nxv 3nxx 3nxy 3nzd 3s3v 3s7a 4ddr 4g95 4kak 4kbn 4kd7 4keb 4kfj 4m6j 4m6k 4m6l 4qhv 4qjc 5hpb 5hqy 5hqz 5hsr 5hsu 5ht4 5ht5 5hui 5hvb 5hve

(-) Related Entries Specified in the PDB File

3l3w