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(-) Description

Title :  CRYSTAL STRUCTURE OF N23PP/S148A MUTANT OF E. COLI DIHYDROFOLATE REDUCTASE
 
Authors :  G. Bhabha, D. C. Ekiert, P. E. Wright, I. A. Wilson
Date :  02 Feb 11  (Deposition) - 20 Apr 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Bhabha, J. Lee, D. C. Ekiert, J. Gam, I. A. Wilson, H. J. Dyson, S. J. Benkovic, P. E. Wright
A Dynamic Knockout Reveals That Conformational Fluctuations Influence The Chemical Step Of Enzyme Catalysis.
Science V. 332 234 2011
PubMed-ID: 21474759  |  Reference-DOI: 10.1126/SCIENCE.1198542

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FOLA, UTI89_C0054
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 364106
    Strain: UTI89 / UPEC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1FOL1Ligand/IonFOLIC ACID
2NA3Ligand/IonSODIUM ION
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:5 , ALA A:6 , ALA A:7 , MET A:20 , ASP A:27 , LEU A:28 , PHE A:31 , LYS A:32 , ILE A:50 , ARG A:57 , ILE A:94 , TYR A:100 , THR A:113 , NAP A:161 , HOH A:180 , HOH A:183 , HOH A:216 , HOH A:226 , HOH A:232 , HOH A:239 , HOH A:268 , HOH A:274 , HOH A:277BINDING SITE FOR RESIDUE FOL A 160
2AC2SOFTWAREALA A:6 , ALA A:7 , ILE A:14 , GLY A:15 , ASN A:18 , ALA A:19 , MET A:20 , GLY A:43 , ARG A:44 , HIS A:45 , THR A:46 , LEU A:62 , SER A:63 , SER A:64 , GLN A:65 , LYS A:76 , ILE A:94 , GLY A:96 , GLY A:97 , ARG A:98 , VAL A:99 , TYR A:100 , GLN A:102 , THR A:123 , FOL A:160 , HOH A:199 , HOH A:217 , HOH A:229 , HOH A:236 , HOH A:246 , HOH A:250 , HOH A:259 , HOH A:281 , HOH A:309 , HOH A:351 , HOH A:358BINDING SITE FOR RESIDUE NAP A 161
3AC3SOFTWAREASP A:87 , ASP A:116 , SER A:150 , HOH A:177 , HOH A:223 , HOH A:255 , HOH A:286BINDING SITE FOR RESIDUE NA A 162
4AC4SOFTWARESER A:135 , HOH A:170 , HOH A:171 , HOH A:174 , HOH A:175 , HOH A:209 , HOH A:210BINDING SITE FOR RESIDUE NA A 163
5AC5SOFTWAREASP A:87 , ASP A:116BINDING SITE FOR RESIDUE NA A 164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QL0)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QL0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QL0)

(-) Exons   (0, 0)

(no "Exon" information available for 3QL0)

(-) 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:160
 aligned with Q1RGF0_ECOUT | Q1RGF0 from UniProtKB/TrEMBL  Length:204

    Alignment length:160
                                                   69                                                                                                                                       
                                                 68 |                                                                                                                                       
                                    55        65  | |   74        84        94       104       114       124       134       144       154       164       174       184       194       204
         Q1RGF0_ECOUT    46 MISLIAALAVDRVIGMENAMPWN-LPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 204
               SCOP domains d3ql0a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains DHFR_1-3ql0A01 A:1-158                                                                                                                                         - Pfam domains
         Sec.struct. author .eeeeeeehhh.eee.........hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee..........eee.hhhhhhhhh.....eee..hhhhhhhhh..eeeeeeeee.......ee....hhh.eeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ql0 A   1 MISLIAALAVDRVIGMENAMPWPPLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNAHSYCFEILERR 159
                                    10        20   |    29        39        49        59        69        79        89        99       109       119       129       139       149       159
                                                 23A
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "CATH Domain" information available for 3QL0)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q1RGF0_ECOUT | Q1RGF0)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.

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3ql3