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(-) Description

Title :  M. TUBERCULOSIS 1-DEOXY-D-XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE BOUND TO 1-DEOXY-L-ERYTHRULOSE
 
Authors :  A. M. Gulick, C. L. Allen, S. A. Kholodar, A. S. Murkin
Date :  17 Sep 14  (Deposition) - 18 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Reductoisomerase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Kholodar, C. L. Allen, A. M. Gulick, A. S. Murkin
The Role Of Phosphate In A Multistep Enzymatic Reaction: Reactions Of The Substrate And Intermediate In Pieces.
J. Am. Chem. Soc. V. 137 2748 2015
PubMed-ID: 25642788  |  Reference-DOI: 10.1021/JA512911F

(-) 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, P425_02990, RVBD_2870C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
    Strain: H37RV
    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  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1DE21Ligand/Ion1-DEOXY-L-ERYTHRULOSE
2MN2Ligand/IonMANGANESE (II) ION
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4PO32Ligand/IonPHOSPHITE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:151 , GLU A:153 , GLU A:222 , DE2 A:403BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWAREGLY 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 , LEU A:108 , ALA A:126 , ASN A:127 , LYS A:128 , GLU A:129 , ASP A:151 , ASN A:209 , MET A:267 , DE2 A:403 , HOH A:501 , HOH A:502 , HOH A:521 , HOH A:573BINDING SITE FOR RESIDUE NDP A 402
3AC3SOFTWARELYS A:128 , ASP A:151 , SER A:152 , GLU A:153 , ASN A:209 , SER A:213 , ASN A:218 , GLU A:222 , MN A:401 , NDP A:402BINDING SITE FOR RESIDUE DE2 A 403
4AC4SOFTWAREALA A:176 , SER A:177 , SER A:213 , ASN A:218 , LYS A:219 , HOH A:538 , HOH A:544 , HOH A:562BINDING SITE FOR RESIDUE PO3 A 404
5AC5SOFTWAREASP B:151 , GLU B:153 , GLU B:222BINDING SITE FOR RESIDUE MN B 401
6AC6SOFTWAREGLY B:19 , THR B:21 , GLY B:22 , SER B:23 , ILE B:24 , GLY B:47 , GLY B:48 , ALA B:49 , HIS B:50 , ALA B:103 , LEU B:104 , VAL B:105 , HOH B:507BINDING SITE FOR RESIDUE NDP B 402
7AC7SOFTWAREALA B:176 , SER B:177 , SER B:213 , ASN B:218 , LYS B:219BINDING SITE FOR RESIDUE PO3 B 403

(-) SS Bonds  (0, 0)

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

(-) 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 4RCV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RCV)

(-) 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               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.hhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh.eeeeeeee........hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh................eeeee........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rcv A  12 RLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGPMNTLNSASLVNKGLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVDDVLDAQRWARERAQRAVSGM 389
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
                                                                                                                                                                                                                    198|                                                                                                                                                                                      
                                                                                                                                                                                                                     207                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:377
                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhh...eee.hhhhhh......ee..hhhhhhhhhh...eeee...hhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh.eeeeeeee........hhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh................eeeeeee......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rcv B  11 GRLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGATWSMGPMNTLNSASLVNKGLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVDDVLDAQRWARERAQRAVSGM 389
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       
                                                                                                                                                                                                                      199|                                                                                                                                                                                           
                                                                                                                                                                                                                       202
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4oof
        I6YAH0_MYCTU | I6YAH0: 4ooe 4oof

(-) Related Entries Specified in the PDB File

4ooe 4oof