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(-) Description

Title :  1-DEOXY-D-XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE
 
Authors :  K. Reuter, S. Sanderbrand, H. Jomaa, J. Wiesner, I. Steinbrecher, E. Be M. Hintz, G. Klebe, M. T. Stubbs
Date :  10 Oct 01  (Deposition) - 27 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alpha-Helix, Beta-Barrel, Dinucleotide Binding Motif, Variable Loop, Induced Fit, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Reuter, S. Sanderbrand, H. Jomaa, J. Wiesner, I. Steinbrecher, E. Beck, M. Hintz, G. Klebe, M. T. Stubbs
Crystal Structure Of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase, A Crucial Enzyme In The Non-Mevalonate Pathway Of Isoprenoid Biosynthesis.
J. Biol. Chem. V. 277 5378 2002
PubMed-ID: 11741911  |  Reference-DOI: 10.1074/JBC.M109500200

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE
    Cellular Location: CHROMOSOMAL DNA
    Chains: A, B, C
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE9
    Expression System Strain: XL1-BLUE PREP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DXR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: DXP REDUCTOISOMERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1K5H)

(-) Sites  (0, 0)

(no "Site" information available for 1K5H)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:15 -A:207

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:188 -Pro A:189
2Trp A:286 -Pro A:287
3Trp B:286 -Pro B:287
4Trp C:286 -Pro C:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K5H)

(-) Exons   (0, 0)

(no "Exon" information available for 1K5H)

(-) 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:398
 aligned with DXR_ECOLI | P45568 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    10        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       390        
            DXR_ECOLI     1 MKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPNWSMGRKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMDMREPQCVDDVLSVDANAREVARKEVMRLAS 398
               SCOP domains d1k5ha2 A:1-125,A:275-300 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                    d1k5ha3 A:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1k5ha2 A:1-125,A:275-300 d1k5ha1 A:301-398 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain               SCOP domains
               CATH domains 1k5hA01 A:1-150 NAD(P)-binding Rossmann-like Domain                                                                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------1k5hA03 A:312-398  [code=1.10.1740.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhh.....eeeehhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhh.hhhhhh......hhhh.eeeeeeee.......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k5h A   1 MKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPNWSMGRKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMDMREPQCVDDVLSVDANAREVARKEVMRLAS 398
                                    10        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       390        


Chain B from PDB  Type:PROTEIN  Length:391
 aligned with DXR_ECOLI | P45568 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:396
                                    10        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       390      
            DXR_ECOLI     1 MKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPNWSMGRKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMDMREPQCVDDVLSVDANAREVARKEVMRL 396
               SCOP domains d1k5hb2 B:1-125,B:275-300 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                    d1k5hb3 B:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1k5hb2 B:1-125,B:275-300 d1k5hb1 B:301-396 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C -terminal domain            SCOP domains
               CATH domains 1k5hB01 B:1-150 NAD(P)-binding Rossmann-like Domain                                                                                                   -------------------------------------------------------------    ------------------------------------------------------------------------------------------------1k5hB03 B:312-396  [code=1.10.1740.10, no name defined]                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh.....eeeehhhhhhhhh......eeee...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh......hhhh.eeeeeeee........hhhhhhhhhhhhh.....----.hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...-....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1k5h B   1 MKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPN----RKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMD-REPQCVDDVLSVDANAREVARKEVMRL 396
                                    10        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       390      
                                                                                                                                                                                                                                            211  216                                                                                                                                                     368 |                          
                                                                                                                                                                                                                                                                                                                                                                                                           370                          


Chain C from PDB  Type:PROTEIN  Length:398
 aligned with DXR_ECOLI | P45568 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    10        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       390        
            DXR_ECOLI     1 MKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPNWSMGRKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMDMREPQCVDDVLSVDANAREVARKEVMRLAS 398
               SCOP domains d1k5hc2 C:1-125,C:275-300 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                    d1k5hc3 C:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1k5hc2 C:1-125,C:275-300 d1k5hc1 C:301-398 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain               SCOP domains
               CATH domains 1k5hC01 C:1-150 NAD(P)-binding Rossmann-like Domain                                                                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------1k5hC03 C:312-398  [code=1.10.1740.10, no name defined]                                 CATH domains
           Pfam domains (1) ---DXP_reductoisom-1k5hC04 C:4-132                                                                                                  -------------DXP_redisom_C-1k5hC01 C:146-239                                                               -------------------------------DXPR_C-1k5hC07 C:271-389                                                                                               --------- Pfam domains (1)
           Pfam domains (2) ---DXP_reductoisom-1k5hC05 C:4-132                                                                                                  -------------DXP_redisom_C-1k5hC02 C:146-239                                                               -------------------------------DXPR_C-1k5hC08 C:271-389                                                                                               --------- Pfam domains (2)
           Pfam domains (3) ---DXP_reductoisom-1k5hC06 C:4-132                                                                                                  -------------DXP_redisom_C-1k5hC03 C:146-239                                                               -------------------------------DXPR_C-1k5hC09 C:271-389                                                                                               --------- Pfam domains (3)
         Sec.struct. author .eeeeee...hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhh.......eehhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhh.hhhhhh......hhhh.eeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k5h C   1 MKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRMVEQCLEFSPRYAVMDDEASAKLLKTMLQQQGSRTEVLSGQQAACDMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFMDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATMTPDQACRHPNWSMGRKISVDSATMMNKGLEYIEARWLFNASASQMEVLIHPQSVIHSMVRYQDGSVLAQLGEPDMRTPIAHTMAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKMDMREPQCVDDVLSVDANAREVARKEVMRLAS 398
                                    10        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       390
   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  (3, 9)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 9)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: DXPR_C] (19)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DXR_ECOLI | P45568)
molecular function
    GO:0030604    1-deoxy-D-xylulose-5-phosphate reductoisomerase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0051484    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway that contributes to terpenoid biosynthesis. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    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:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DXR_ECOLI | P45568: 1jvs 1onn 1ono 1onp 1q0h 1q0l 1q0q 1t1r 1t1s 2egh 3anl 3anm 3ann 3r0i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K5H)