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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH PYRIMETHAMINE
 
Authors :  M. V. B Dias, P. Tyrakis, T. L. Blundell
Date :  07 May 13  (Deposition) - 25 Dec 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Dias, P. Tyrakis, R. R. Domingues, A. F. Paes Leme, T. L. Blundell
Mycobacterium Tuberculosis Dihydrofolate Reductase Reveals Two Conformational States And A Possible Low Affinity Mechanism To Antifolate Drugs.
Structure V. 22 94 2014
PubMed-ID: 24210757  |  Reference-DOI: 10.1016/J.STR.2013.09.022

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET28A
    Gene: DFRA, FOLA, MT2833, MTV002.28C, RV2763C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV

 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
1ATR2Ligand/Ion2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2CP62Ligand/Ion5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ATR1Ligand/Ion2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2CP61Ligand/Ion5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ATR1Ligand/Ion2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2CP61Ligand/Ion5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:5 , TRP A:6 , ALA A:7 , ASP A:27 , PHE A:31 , THR A:46 , LEU A:50 , ILE A:94 , HOH A:307 , HOH A:437BINDING SITE FOR RESIDUE CP6 A 201
2AC2SOFTWAREGLY A:43 , ARG A:44 , ARG A:45 , THR A:46 , LEU A:65 , SER A:66 , ARG A:67 , GLN A:68 , GLY A:80 , GLY A:96 , GLY A:97 , GLN A:98 , VAL A:99 , LEU A:102 , HOH A:355 , HOH A:356 , HOH A:388 , HOH A:409 , HOH A:419 , HOH A:446 , HOH A:491BINDING SITE FOR RESIDUE ATR A 202
3AC3SOFTWAREILE B:5 , TRP B:6 , ALA B:7 , ILE B:20 , ASP B:27 , GLN B:28 , PHE B:31 , THR B:46 , LEU B:50 , ILE B:94 , TYR B:100 , HOH B:473 , HOH B:519BINDING SITE FOR RESIDUE CP6 B 201
4AC4SOFTWAREARG B:32 , GLY B:43 , ARG B:44 , ARG B:45 , THR B:46 , LEU B:65 , SER B:66 , ARG B:67 , GLN B:68 , GLY B:80 , GLY B:96 , GLY B:97 , GLN B:98 , VAL B:99 , LEU B:102 , HOH B:317 , HOH B:366 , HOH B:379 , HOH B:386 , HOH B:472 , HOH B:505BINDING SITE FOR RESIDUE ATR B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KM0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:55 -Pro A:56
2Gly A:95 -Gly A:96
3Arg B:55 -Pro B:56
4Gly B:95 -Gly B:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KM0)

(-) Exons   (0, 0)

(no "Exon" information available for 4KM0)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains d4km0a_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhh..........eeeee...........eee.hhhhhh...eeeeeehhhhhhhhhhhh.eeeeeee..........ee........eeee...ee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4km0 A  -1 SHMVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 


Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d4km0b_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhh..........eeeee...........eee.hhhhhh...eeeeeehhhhhhhhhhhh.eeeeeee..........ee........eeee...ee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4km0 B  -1 SHMVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KM0)

(-) Gene Ontology  (9, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:55 - Pro A:56   [ RasMol ]  
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  DYR_MYCTU | P9WNX1
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  1.5.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        DYR_MYCTO | P9WNX0: 1df7 1dg5 1dg7 1dg8 2cig 4kl9 4klx 4km2 4kne 4m2x 5ja3
        DYR_MYCTU | P9WNX1: 1df7 1dg5 1dg7 1dg8 2cig 4kl9 4klx 4km2 4kne 4m2x 5ja3 5u26 5u27 5ujf

(-) Related Entries Specified in the PDB File

4kl9 4klx 4km2 4kne