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(-) Description

Title :  DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEXED WITH 5,10-DIDEAZATETRAHYDROFOLATE
 
Authors :  M. R. Sawaya
Date :  19 Sep 96  (Deposition) - 11 Jan 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxido-Reductase, Nadp, Trimethoprim Resistance, Methotrexate Resistance, One-Carbon Metabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Sawaya, J. Kraut
Loop And Subdomain Movements In The Mechanism Of Escherichia Coli Dihydrofolate Reductase: Crystallographic Evidence.
Biochemistry V. 36 586 1997
PubMed-ID: 9012674  |  Reference-DOI: 10.1021/BI962337C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRWA-1
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: RT500
    Synonym: DHFR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DDF1Ligand/Ion5,10-DIDEAZATETRAHYDROFOLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:5 , ALA A:6 , ALA A:7 , ASP A:27 , PHE A:31 , LYS A:32 , ARG A:52 , ARG A:57 , ILE A:94 , TYR A:100 , THR A:113 , HOH A:300 , HOH A:321 , HOH A:331 , HOH A:339BINDING SITE FOR RESIDUE DDF A 161

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RX5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:95 -Gly A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DYR_ECOLI_001 *L28RDYR_ECOLI  ---  ---AL28R
2UniProtVAR_DYR_ECOLI_002 *W30GDYR_ECOLI  ---  ---AW30G
3UniProtVAR_DYR_ECOLI_003 *E154KDYR_ECOLI  ---  ---AE154K
4UniProtVAR_DYR_ECOLI_004 *E154QDYR_ECOLI  ---  ---AE154Q
   * ID not provided by source
  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_ECOLI1-158  1A:1-158
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_ECOLI13-35  1A:13-35

(-) Exons   (0, 0)

(no "Exon" information available for 1RX5)

(-) 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:159
 aligned with DYR_ECOLI | P0ABQ4 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
            DYR_ECOLI     1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
               SCOP domains d1rx5a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains 1rx5A00 A:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...................hhhhhhhhhhh...eeeeehhhhhhh.......eeeee..........eee..hhhhhhhh.....eeeee.hhhhhhhhhheeeeeeeee.................eee...............eeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------R-G---------------------------------------------------------------------------------------------------------------------------K----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------Q----- SAPs(SNPs) (2)
                PROSITE (1) DHFR_2  PDB: A:1-158 UniProt: 1-158                                                                                                                           - PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: A:13-35   ---------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rx5 A   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    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 1RX5)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DYR_ECOLI | P0ABQ4)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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: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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_ECOLI | P0ABQ4: 1ddr 1dds 1dhi 1dhj 1dra 1drb 1dre 1drh 1dyh 1dyi 1dyj 1jol 1jom 1ra1 1ra2 1ra3 1ra8 1ra9 1rb2 1rb3 1rc4 1rd7 1re7 1rf7 1rg7 1rh3 1rx1 1rx2 1rx3 1rx4 1rx6 1rx7 1rx8 1rx9 1tdr 2ano 2anq 2d0k 2drc 2inq 3dau 3drc 3k74 3kfy 3och 3ql3 3qyl 3qyo 3r33 4dfr 4eig 4eiz 4ej1 4fhb 4gh8 4i13 4i1n 4kjj 4kjk 4kjl 4nx6 4nx7 4pdj 4x5f 4x5g 4x5h 4x5i 4x5j 5cc9 5ccc 5dfr 5e8q 5eaj 6dfr 7dfr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RX5)