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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF DIHYDROFOLATE REDUCTASE FROM BACTERIOPHAGE T4
 
Authors :  J. H. Moon, Y. K. Oh, S. W. Suh
Date :  28 Aug 01  (Deposition) - 23 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Complexed With Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Moon, Y. K. Oh, J. Y. Lee, S. W. Suh
Crystal Structure Analysis Of Dihydrofolate Reductase From Bacteriophage T4
To Be Published
PubMed: search
(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: PET22B
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FRD
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: DHFR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:6 , ARG A:7 , PHE A:22 , GLY A:23 , LEU A:24 , GLY A:25 , GLY A:27 , TRP A:30 , GLY A:52 , ALA A:53 , LYS A:54 , THR A:55 , CYS A:72 , ASP A:73 , ARG A:76 , ASP A:77 , PRO A:79 , GLY A:128 , GLY A:129 , PRO A:130 , HOH A:199 , HOH A:224 , HOH A:251 , HOH A:257 , HOH A:289 , HOH A:295BINDING SITE FOR RESIDUE NDP A 194

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JUV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JUV)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_BPT41-193  1A:1-193
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_BPT421-44  1A:21-44
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_BPT41-193  2A:1-193
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_BPT421-44  2A:21-44

(-) Exons   (0, 0)

(no "Exon" information available for 1JUV)

(-) Sequences/Alignments

Asymmetric Unit
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  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:193
 aligned with DYR_BPT4 | P04382 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
             DYR_BPT4     1 MIKLVFRYSPTKTVDGFNELAFGLGDGLPWGRVKKDLQNFKARTEGTIMIMGAKTFQSLPTLLPGRSHIVVCDLARDYPVTKDGDLAHFYITWEQYITYISGGEIQVSSPNAPFETMLDQNSKVSVIGGPALLYAALPYADEVVVSRIVKRHRVNSTVQLDASFLDDISKREMVETHWYKIDEVTTLTESVYK 193
               SCOP domains d1juva_ A: Dihydrofolate reductase, prokaryotic type                                                                                                                                              SCOP domains
               CATH domains 1juvA00 A:1-193 Dihydrofolate Reductase, subunit A                                                                                                                                                CATH domains
               Pfam domains -----------------DHFR_1-1juvA01 A:18-188                                                                                                                                                    ----- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeeee.........hhhhhhhhhhhhh..eeeeehhhhhh.........eeee.................eeehhhhhhhhhh...eeee......eeee.....eeeeehhhhhhhhhhhh.eeeeeeeee.......eeehhhhhhhhhh..eeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DHFR_2  PDB: A:1-193 UniProt: 1-193                                                                                                                                                               PROSITE (1)
                PROSITE (2) --------------------DHFR_1  PDB: A:21-44    ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1juv A   1 MIKLVFRYSPTKTVDGFNELAFGLGDGLPWGRVKKDLQNFKARTEGTIMIMGAKTFQSLPTLLPGRSHIVVCDLARDYPVTKDGDLAHFYITWEQYITYISGGEIQVSSPNAPFETMLDQNSKVSVIGGPALLYAALPYADEVVVSRIVKRHRVNSTVQLDASFLDDISKREMVETHWYKIDEVTTLTESVYK 193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (DYR_BPT4 | P04382)
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: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: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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  1juv
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