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(-) Description

Title :  M. TUBERCULOSIS 1-DEOXY-D-XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE W203F MUTANT BOUND TO FOSMIDOMYCIN AND NADPH
 
Authors :  C. L. Allen, S. A. Kholodar, A. S. Murkin, A. M. Gulick
Date :  31 Jan 14  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Reductoisomerase, Oxidoreductase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Kholodar, G. Tombline, J. Liu, Z. Tan, C. L. Allen, A. M. Gulick, A. S. Murkin
Alteration Of The Flexible Loop In 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase Boosts Enthalpy-Driven Inhibition By Fosmidomycin.
Biochemistry V. 53 3423 2014
PubMed-ID: 24825256  |  Reference-DOI: 10.1021/BI5004074

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
    Chains: A, B
    EC Number: 1.1.1.267
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-389
    Gene: DXR, RVBD_2870C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: HRV37
    Synonym: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE REDUCTOISOMERASE, 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FOM2Ligand/Ion3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
2MN2Ligand/IonMANGANESE (II) ION
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , THR A:21 , GLY A:22 , SER A:23 , ILE A:24 , ALA A:46 , GLY A:47 , GLY A:48 , ALA A:49 , HIS A:50 , ALA A:69 , ALA A:103 , LEU A:104 , VAL A:105 , LEU A:108 , ALA A:126 , ASN A:127 , LYS A:128 , GLU A:129 , ASP A:151 , MET A:205 , GLY A:206 , PRO A:207 , ASN A:209 , MET A:267 , FOM A:402 , HOH A:501 , HOH A:511 , HOH A:532 , HOH A:541 , HOH A:560 , HOH A:579 , HOH A:583 , HOH A:621 , HOH A:636BINDING SITE FOR RESIDUE NDP A 400
2AC2SOFTWARELYS A:128 , ASP A:151 , GLU A:153 , GLU A:222 , FOM A:402BINDING SITE FOR RESIDUE MN A 401
3AC3SOFTWARELYS A:128 , ASP A:151 , SER A:152 , GLU A:153 , ALA A:176 , SER A:177 , HIS A:200 , PHE A:203 , MET A:205 , SER A:213 , ASN A:218 , LYS A:219 , GLU A:222 , NDP A:400 , MN A:401 , HOH A:506 , HOH A:509 , HOH A:530BINDING SITE FOR RESIDUE FOM A 402
4AC4SOFTWAREGLY B:19 , THR B:21 , GLY B:22 , SER B:23 , ILE B:24 , ALA B:46 , GLY B:47 , GLY B:48 , ALA B:49 , HIS B:50 , ALA B:69 , ALA B:103 , LEU B:104 , VAL B:105 , LEU B:108 , ALA B:126 , ASN B:127 , LYS B:128 , GLU B:129 , ASP B:151 , MET B:205 , GLY B:206 , ASN B:209 , MET B:267 , FOM B:402 , HOH B:504 , HOH B:506 , HOH B:531 , HOH B:565 , HOH B:570 , HOH B:600 , HOH B:640 , HOH B:656 , HOH B:663BINDING SITE FOR RESIDUE NDP B 400
5AC5SOFTWAREASP B:151 , GLU B:153 , GLU B:222 , FOM B:402BINDING SITE FOR RESIDUE MN B 401
6AC6SOFTWAREASP B:151 , SER B:152 , GLU B:153 , ALA B:176 , SER B:177 , HIS B:200 , PHE B:203 , MET B:205 , SER B:213 , ASN B:218 , LYS B:219 , GLU B:222 , NDP B:400 , MN B:401 , HOH B:503 , HOH B:514 , HOH B:517BINDING SITE FOR RESIDUE FOM B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:277 -Pro A:278
2Trp B:277 -Pro B:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OOF)

(-) 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:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhh...eee.hhhhhhhhh...ee..hhhhhhhhh....eeee...hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh.eeeeeeee........hhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh................eeeee........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oof A  11 GRLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGAHPTFSMGPMNTLNSASLVNKGLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVDDVLDAQRWARERAQRAVSG 388
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380        


Chain B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh...eee.hhhhhhhhh...ee..hhhhhhhhhh...eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhh.eeeeeeee........hhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh................eeeee........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oof B  11 GRLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGAHPTFSMGPMNTLNSASLVNKGLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVDDVLDAQRWARERAQRAVSG 388
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380
   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  (0, 0)

(no "SCOP Domain" information available for 4OOF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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    Trp A:277 - Pro A:278   [ RasMol ]  
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  4oof
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  DXR_MYCTU | P9WNS1
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  I6YAH0_MYCTU | I6YAH0
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  1.1.1.267
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 Related Entries

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

UniProtKB/Swiss-Prot
        DXR_MYCTU | P9WNS1: 2c82 2jcv 2jcx 2jcy 2jd0 2jd1 2jd2 2y1c 2y1d 2y1e 2y1f 2y1g 3ras 3zhx 3zhy 3zhz 3zi0 4a03 4aic 4ooe 4rcv
        I6YAH0_MYCTU | I6YAH0: 4ooe 4rcv

(-) Related Entries Specified in the PDB File

3zhx DXR
4aic DXR
4ooe