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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOMETHIONINE-LABELLED DXR IN COMPLEX WITH FOSMIDOMYCIN
 
Authors :  A. Mac Sweeney, R. Lange, A. D'Arcy, A. Douangamath, J. -P. Surivet, C.
Date :  16 Jul 03  (Deposition) - 20 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mac Sweeney, R. Lange, R. P. Fernandes, H. Schulz, G. E. Dale, A. Douangamath, P. J. Proteau, C. Oefner
The Crystal Structure Of E. Coli 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase In A Ternar Complex With The Antimalarial Compound Fosmidomycin And Nadph Reveals A Tight-Binding Closed Enzyme Conformation.
J. Mol. Biol. V. 345 115 2005
PubMed-ID: 15567415  |  Reference-DOI: 10.1016/J.JMB.2004.10.030

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
    Chains: A
    EC Number: 1.1.1.267
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDS-6HISNDEI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DXR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE REDUCTOISOMERASE, ISPC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2FOM1Ligand/Ion3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
3MSE19Mod. Amino AcidSELENOMETHIONINE
4NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (4, 44)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2FOM2Ligand/Ion3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
3MSE38Mod. Amino AcidSELENOMETHIONINE
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:151 , GLU A:152 , GLY A:185 , SER A:186 , HIS A:209 , SER A:222 , ASN A:227 , LYS A:228 , GLU A:231 , MSE A:276 , HOH A:415 , HOH A:464 , HOH A:653BINDING SITE FOR RESIDUE FOM A 400
2AC2SOFTWAREGLY A:8 , THR A:10 , GLY A:11 , SER A:12 , ILE A:13 , ALA A:35 , GLY A:36 , LYS A:37 , ASN A:38 , ASP A:57 , ILE A:101 , VAL A:102 , MSE A:214 , GLY A:215 , ARG A:216 , LYS A:217 , HOH A:413 , HOH A:429 , HOH A:559 , HOH A:581 , HOH A:587 , HOH A:618 , HOH A:647BINDING SITE FOR RESIDUE NDP A 401
3AC3SOFTWARECYS A:15 , ARG A:41 , ARG A:352 , ALA A:397 , SER A:398 , HOH A:483 , HOH A:629BINDING SITE FOR RESIDUE CIT A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q0H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:184 -Gly A:185
2Trp A:286 -Pro A:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q0H)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q0H)

(-) 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 d1q0ha2 A:1-125,A:275-300 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                    d1q0ha3 A:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1q0ha2 A:1-125,A:275-300 d1q0ha1 A:301-398 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain               SCOP domains
               CATH domains -1q0hA01 A:2-150 NAD(P)-binding Rossmann-like Domain                                                                                                  -----------------------------------------------------------------------------------------------------------------------------------------------------------------1q0hA03 A:312-398  [code=1.10.1740.10, no name defined]                                 CATH domains
               Pfam domains ---DXP_reductoisom-1q0hA02 A:4-132                                                                                                  -------------DXP_redisom_C-1q0hA01 A:146-239                                                               -------------------------------DXPR_C-1q0hA03 A:271-389                                                                                               --------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...eeeehhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhh.hhhhhh......hhhh.eeeeeeee........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0h 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   |    
                            |                                       42-MSE        56-MSE      68-MSE              88-MSE    98-MSE                               136-MSE                                                          201-MSE      214-MSE    225-MSE              246-MSE      259-MSE          276-MSE 284-MSE                               322-MSE                                      367-MSE                    394-MSE
                            1-MSE                                                                                                                                                                                                                          226-MSE                                                                                                                                        369-MSE
   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, 3)

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, 2)

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

(-) Pfam Domains  (3, 3)

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   (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 1k5h 1onn 1ono 1onp 1q0l 1q0q 1t1r 1t1s 2egh 3anl 3anm 3ann 3r0i

(-) Related Entries Specified in the PDB File

1q0l CRYSTAL STRUCTURE OF DXR IN COMPLEX WITH FOSMIDOMYCIN
1q0q CRYSTAL STRUCTURE OF DXR IN COMPLEX WITH THE SUBSTRATE 1- DEOXY-D-XYLULOSE-5-PHOSPHATE