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(-) Description

Title :  CANDIDA GLABRATA DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 2,4-DIAMINO-5-(3-(2,5-DIMETHOXYPHENYL)PROP-1-YNYL)-6-ETHYLPYRIMIDINE (UCP120B)
 
Authors :  J. Liu, A. C. Anderson
Date :  09 Apr 08  (Deposition) - 25 Nov 08  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Ligand Complex, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, D. B. Bolstad, A. E. Smith, N. D. Priestley, D. L. Wright, A. C. Anderson
Structure-Guided Development Of Efficacious Antifungal Agents Targeting Candida Glabrata Dihydrofolate Reductase.
Chem. Biol. V. 15 990 2008
PubMed-ID: 18804036  |  Reference-DOI: 10.1016/J.CHEMBIOL.2008.07.013

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHFR
    Organism Common: YEAST
    Organism Scientific: CANDIDA GLABRATA
    Organism Taxid: 5478

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1N222Ligand/Ion5-[3-(2,5-DIMETHOXYPHENYL)PROP-1-YN-1-YL]-6-ETHYLPYRIMIDINE-2,4-DIAMINE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1N221Ligand/Ion5-[3-(2,5-DIMETHOXYPHENYL)PROP-1-YN-1-YL]-6-ETHYLPYRIMIDINE-2,4-DIAMINE
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1N221Ligand/Ion5-[3-(2,5-DIMETHOXYPHENYL)PROP-1-YN-1-YL]-6-ETHYLPYRIMIDINE-2,4-DIAMINE
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:10 , ALA A:11 , ILE A:19 , GLY A:20 , GLY A:23 , ASN A:24 , LEU A:25 , GLY A:55 , ARG A:56 , LYS A:57 , THR A:58 , VAL A:77 , SER A:78 , ARG A:79 , ASN A:96 , SER A:97 , LEU A:98 , ILE A:121 , GLY A:123 , GLY A:124 , GLU A:125 , ILE A:126 , TYR A:127 , GLN A:129 , N22 A:302 , HOH A:419 , HOH A:433 , HOH A:444 , HOH A:447 , HOH A:511 , HOH A:519 , HOH A:556BINDING SITE FOR RESIDUE NDP A 301
2AC2SOFTWAREILE A:9 , VAL A:10 , ALA A:11 , LEU A:25 , GLU A:32 , MET A:33 , PHE A:36 , SER A:61 , ILE A:62 , ILE A:121 , TYR A:127 , THR A:140 , NDP A:301 , HOH A:433 , HOH A:545BINDING SITE FOR RESIDUE N22 A 302
3AC3SOFTWAREVAL B:10 , ALA B:11 , ILE B:19 , GLY B:20 , GLY B:23 , ASN B:24 , LEU B:25 , GLY B:55 , ARG B:56 , LYS B:57 , THR B:58 , VAL B:77 , SER B:78 , ARG B:79 , ASN B:96 , SER B:97 , LEU B:98 , ILE B:121 , GLY B:123 , GLY B:124 , GLU B:125 , ILE B:126 , TYR B:127 , GLN B:129 , N22 B:302 , HOH B:426 , HOH B:460 , HOH B:463 , HOH B:490 , HOH B:494 , HOH B:507 , HOH B:583 , HOH B:589BINDING SITE FOR RESIDUE NDP B 301
4AC4SOFTWAREILE B:9 , VAL B:10 , ALA B:11 , LEU B:25 , GLU B:32 , MET B:33 , PHE B:36 , SER B:61 , LEU B:69 , ILE B:121 , TYR B:127 , THR B:140 , NDP B:301 , HOH B:463 , HOH B:543BINDING SITE FOR RESIDUE N22 B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Leu A:14 -Pro A:15
2Arg A:67 -Pro A:68
3Gly A:122 -Gly A:123
4Leu B:14 -Pro B:15
5Arg B:67 -Pro B:68
6Gly B:122 -Gly B:123
7Asn B:193 -Gly B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CSE)

(-) Sequences/Alignments

Asymmetric 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:225
 aligned with Q6FPH0_CANGA | Q6FPH0 from UniProtKB/TrEMBL  Length:217

    Alignment length:225
                                                                                                                                                                                                                                                217          
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    |    -     
         Q6FPH0_CANGA     3 KVPVVGIVAALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGRKTWESIPQKFRPLPKRINVVVSRSFDGELRKVEDGIYHSNSLRNCLTALQSSLANENKIERIYIIGGGEIYRQSMDLADHWLITKIMPLPETTIPQMDTFLQKQELEQRFYDNSDKLVDFLPSSIQLEGRLTSQEWNGELVKGLPVQEKGYQFYFTLYTKK----------   -
               SCOP domains d3csea_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                                                              SCOP domains
               CATH domains 3cseA00 A:3-227 Dihydrofolate Reductase, subunit A                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eee........hhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh.....eeeee........eeee..eeee.hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh....eeeeeeeee..........ee.hhhhhhhheee...hhhhhh..........eeeee..eeeeeeeeee..eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cse A   3 KVPVVGIVAALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGRKTWESIPQKFRPLPKRINVVVSRSFDGELRKVEDGIYHSNSLRNCLTALQSSLANENKIERIYIIGGGEIYRQSMDLADHWLITKIMPLPETTIPQMDTFLQKQELEQRFYDNSDKLVDFLPSSIQLEGRLTSQEWNGELVKGLPVQEKGYQFYFTLYTKKLEHHHHHHHH 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q6FPH0_CANGA | Q6FPH0 from UniProtKB/TrEMBL  Length:217

    Alignment length:225
                                                                                                                                                                                                                                                217          
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    |    -     
         Q6FPH0_CANGA     3 KVPVVGIVAALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGRKTWESIPQKFRPLPKRINVVVSRSFDGELRKVEDGIYHSNSLRNCLTALQSSLANENKIERIYIIGGGEIYRQSMDLADHWLITKIMPLPETTIPQMDTFLQKQELEQRFYDNSDKLVDFLPSSIQLEGRLTSQEWNGELVKGLPVQEKGYQFYFTLYTKK----------   -
               SCOP domains d3cseb_ B: Dihydrofolate reductases, eukaryotic type                                                                                                                                                                              SCOP domains
               CATH domains 3cseB00 B:3-227 Dihydrofolate Reductase, subunit A                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eee........hhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh.....eeeee........eeee..eeee.hhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh....eeeeeeeee..........ee.hhhhhhhheee...hhhhhh..........eeeee..eeeeeeeeee..eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cse B   3 KVPVVGIVAALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGRKTWESIPQKFRPLPKRINVVVSRSFDGELRKVEDGIYHSNSLRNCLTALQSSLANENKIERIYIIGGGEIYRQSMDLADHWLITKIMPLPETTIPQMDTFLQKQELEQRFYDNSDKLVDFLPSSIQLEGRLTSQEWNGELVKGLPVQEKGYQFYFTLYTKKLEHHHHHHHH 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6FPH0_CANGA | Q6FPH0)
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: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: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.
biological process
    GO:0046452    dihydrofolate metabolic process    The chemical reactions and pathways involving dihydrofolate, the dihydroxylated derivative of folate.
    GO:0006760    folic acid-containing compound metabolic process    The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.
    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.
    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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 Related Entries

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        Q6FPH0_CANGA | Q6FPH0: 3eej 3eek 3eel 3eem 3qlx 3qly 3qlz 3ro9 3roa 4h98 4hog

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