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(-) Description

Title :  S. AUREUS DHFR COMPLEXED WITH NADPH AND ICLAPRIM
 
Authors :  C. Oefner, E. Dale-Glenn
Date :  08 Jan 09  (Deposition) - 12 Jan 10  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  X
Keywords :  Dhfr, Oxidoreductase, Nadp, One-Carbon Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Oefner, M. Bandera, A. Haldimann, H. Laue, H. Schulz, S. Mukhija, S. Parisi, L. Weiss, S. Lociuro, G. E. Dale
Increased Hydrophobic Interactions Of Iclaprim With Staphylococcus Aureus Dihydrofolate Reductase Are Responsible For The Increase In Affinity And Antibacterial Activity
J. Antimicrob. Chemother. V. 63 687 2009
PubMed-ID: 19211577  |  Reference-DOI: 10.1093/JAC/DKP024

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: X
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FOLA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: DHFR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2XCF1Ligand/Ion5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5-YL]METHYL]PYRIMIDINE-2,4-DIAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL X:6 , ALA X:7 , ILE X:14 , GLY X:15 , ASN X:18 , GLN X:19 , LEU X:20 , GLY X:43 , ARG X:44 , LYS X:45 , THR X:46 , LEU X:62 , THR X:63 , SER X:64 , HIS X:77 , ILE X:79 , PHE X:92 , GLY X:93 , GLY X:94 , GLN X:95 , THR X:96 , LEU X:97 , GLU X:100 , THR X:121 , HOH X:176 , HOH X:177 , XCF X:300BINDING SITE FOR RESIDUE NDP X 301
2AC2SOFTWARELEU X:5 , VAL X:6 , ALA X:7 , LEU X:20 , ASP X:27 , LEU X:28 , VAL X:31 , SER X:49 , LEU X:54 , PHE X:92 , HOH X:167 , HOH X:253 , NDP X:301BINDING SITE FOR RESIDUE XCF X 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly X:93 -Gly X:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FRF)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_STAAU2-157  1X:1-156
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_STAAU14-36  1X:13-35

(-) Exons   (0, 0)

(no "Exon" information available for 3FRF)

(-) 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 X from PDB  Type:PROTEIN  Length:158
 aligned with DYR_STAAU | P0A017 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
            DYR_STAAU     2 TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK 159
               SCOP domains d3frfx_ X: Dihydrofolate reductase, prokaryotic type                                                                                                           SCOP domains
               CATH domains 3frfX00 X:1-158 Dihydrofolate Reductase, subunit A                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee..........eeee.hhhhh......eeeeehhhhhhhhh....eeeeeee.......ee........eeeeeeee..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DHFR_2  PDB: X:1-156 UniProt: 2-157                                                                                                                         -- PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: X:13-35   --------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3frf X   1 TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (DYR_STAAU | P0A017)
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: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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  1.5.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_STAAU | P0A017: 2w9g 2w9h 3fra 3frb 3frd 3fre 3fy8 3fy9 3fyv 3fyw 3i8a 3lg4 3m08 3m09 3sgy 3sh2 3sqy 3sr5 3srq 3srr 3srs 3sru 3srw 4fgg 4fgh 4lae 4lag 4lah 4lek 4xe6 4xec 5hf0 5hf2 5isp 5isq 5ist 5jg0

(-) Related Entries Specified in the PDB File

3fra 3frb 3frd 3fre