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(-) Description

Title :  LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+
 
Authors :  V. Cody, N. Galitsky, D. Rak, J. R. Luft, W. Pangborn, S. F. Queener
Date :  18 Mar 99  (Deposition) - 29 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxido-Reductase, Folate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Cody, N. Galitsky, D. Rak, J. R. Luft, W. Pangborn, S. F. Queener
Ligand-Induced Conformational Changes In The Crystal Structures Of Pneumocystis Carinii Dihydrofolate Reductase Complexes With Folate And Nadp+.
Biochemistry V. 38 4303 1999
PubMed-ID: 10194348  |  Reference-DOI: 10.1021/BI982728M
(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 Gene: C-DNA P.CARINII DHFR
    Expression System Plasmid: PT7-7
    Expression System Taxid: 562
    Organism Scientific: PNEUMOCYSTIS CARINII
    Organism Taxid: 4754
    Synonym: PCDHFR

 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
1FOL1Ligand/IonFOLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:10 , ALA A:12 , GLU A:32 , ILE A:33 , PHE A:36 , LYS A:37 , PHE A:69 , ARG A:75 , ILE A:123 , TYR A:129 , HOH A:215 , HOH A:216BINDING SITE FOR RESIDUE FOL A 207
2S1AUTHORILE A:10 , LEU A:25 , TRP A:27 , GLU A:32 , ILE A:33 , PHE A:36 , ILE A:65 , PRO A:66 , ILE A:123 , TYR A:129 , THR A:144THE BINDING ORIENTATION OF THE PTERIDINE RING OF FOL IN THIS STRUCTURE IS SIMILAR TO THAT OBSERVED IN HDHFR FA BINARY COMPLEXES.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CD2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:70 -Pro A:71
2Gly A:124 -Gly A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CD2)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_PNECA6-204  1A:6-204
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_PNECA18-40  1A:18-40

(-) Exons   (0, 0)

(no "Exon" information available for 4CD2)

(-) 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:202
 aligned with DYR_PNECA | P16184 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:202
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  
            DYR_PNECA     5 KSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL 206
               SCOP domains d4cd2a_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                                       SCOP domains
               CATH domains 4cd2A00 A:5-206 Dihydrofolate Reductase, subunit A                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...............hhhhhhhhhhhh....hhh.....eeeeehhhhhh...........eeeee............eee..hhhhhhhhhhh...........eeeee.hhhhhhhh....eeeeeeeee................hhh........hhhhhhhh........eee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -DHFR_2  PDB: A:6-204 UniProt: 6-204                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -------------DHFR_1  PDB: A:18-40   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cd2 A   5 KSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL 206
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
   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 4CD2)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DYR_PNECA | P16184)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_PNECA | P16184: 1cd2 1daj 1dyr 1e26 1klk 1ly3 1ly4 1s3y 1vj3 2cd2 2fzh 2fzi 3cd2 3nz6 3nz9 3nza 3nzb 3nzc 3td8 4g8z 4ixe 4ixf 4ixg 4qjz

(-) Related Entries Specified in the PDB File

1cd2 2cd2 3cd2