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(-) Description

Title :  CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE; A TARGET ENZYME FOR ANTIMALARIAL DRUGS
 
Authors :  S. Yajima, T. Nonaka, T. Kuzuyama, H. Seto, K. Ohsawa
Date :  31 Aug 01  (Deposition) - 09 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Reductoisomerase, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yajima, T. Nonaka, T. Kuzuyama, H. Seto, K. Ohsawa
Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase Complexed With Cofactors: Implications Of A Flexible Loop Movement Upon Substrate Binding.
J. Biochem. (Tokyo) V. 131 313 2002
PubMed-ID: 11872159
(for further references see the PDB file header)

(-) 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 Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 40)

Asymmetric/Biological Unit (3, 40)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:184 , SER A:185 , HIS A:208 , SER A:221 , ASN A:226 , LYS A:227 , HOH A:2053 , HOH A:2102BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREGLY B:184 , SER B:185 , HIS B:208 , SER B:221 , ASN B:226 , LYS B:227 , HOH B:2021 , HOH B:2088 , HOH B:2109BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWAREGLY A:7 , THR A:9 , GLY A:10 , SER A:11 , ILE A:12 , ALA A:34 , GLY A:35 , LYS A:36 , ASN A:37 , ASP A:56 , ALA A:99 , ILE A:100 , VAL A:101 , ALA A:104 , ALA A:122 , ASN A:123 , ASP A:149 , MSE A:275 , HOH A:2046 , HOH A:2099 , HOH A:2100BINDING SITE FOR RESIDUE NDP A 2001
4AC4SOFTWAREGLY B:7 , THR B:9 , GLY B:10 , SER B:11 , ILE B:12 , ALA B:34 , GLY B:35 , LYS B:36 , ASN B:37 , ASP B:56 , ALA B:99 , VAL B:101 , ALA B:104 , ALA B:122 , ASN B:123 , LYS B:124 , ASP B:149 , HOH B:2078 , HOH B:2083BINDING SITE FOR RESIDUE NDP B 2002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:285 -Pro A:286
2Trp B:285 -Pro B:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JVS)

(-) 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:400
 aligned with DXR_ECOLI | P45568 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                       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--   -
               SCOP domains d1jvsa2 A:0-125,A:275-300 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                     d1jvsa3 A:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1jvsa2 A:0-125,A:275-300 d1jvsa1 A:301-399 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain                SCOP domains
               CATH domains 1jvsA01 A:0-149 NAD(P)-binding Rossmann-like Domain                                                                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------1jvsA03 A:311-399  [code=1.10.1740.10, no name defined]                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhhh.....eeee......hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhh.hhhhhh......hhhh.eeeeeeee........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvs A   0 GKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRmVEQCLEFSPRYAVmDDEASAKLLKTmLQQQGSRTEVLSGQQAACDmAALEDVDQVmAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFmDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATmTPDQACRHPNWSmGRKISVDSATmmNKGLEYIEARWLFNASASQmEVLIHPQSVIHSmVRYQDGSVLAQLGEPDmRTPIAHTmAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAmEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKmDmREPQCVDDVLSVDANAREVARKEVmRLASSA 399
                                     9        19        29        39 |      49     |  59       |69        79       |89       |99       109       119       129     | 139       149       159       169       179       189       199|      209   |   219    || 229       239     | 249       259       269     | 279   |   289       299       309       319 |     329       339       349       359      |369       379       389   |   399
                                                                    41-MSE        55-MSE      67-MSE              87-MSE    97-MSE                               135-MSE                                                          200-MSE      213-MSE    224-MSE              245-MSE      258-MSE          275-MSE 283-MSE                               321-MSE                                      366-MSE                    393-MSE  
                                                                                                                                                                                                                                                           225-MSE                                                                                                                                        368-MSE                           


Chain B 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 d1jvsb2 B:0-125,B:275-300 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                     d1jvsb3 B:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1jvsb2 B:0-125,B:275-300 d1jvsb1 B:301-397 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain              SCOP domains
               CATH domains 1jvsB01 B:0-149 NAD(P)-binding Rossmann-like Domain                                                                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------1jvsB03 B:311-397  [code=1.10.1740.10, no name defined]                                 CATH domains
           Pfam domains (1) ---DXP_reductoisom-1jvsB03 B:3-131                                                                                                  -------------DXP_redisom_C-1jvsB01 B:145-238                                                               -------------------------------DXPR_C-1jvsB05 B:270-388                                                                                               --------- Pfam domains (1)
           Pfam domains (2) ---DXP_reductoisom-1jvsB04 B:3-131                                                                                                  -------------DXP_redisom_C-1jvsB02 B:145-238                                                               -------------------------------DXPR_C-1jvsB06 B:270-388                                                                                               --------- Pfam domains (2)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhh.hhhhhh......hhhh.eeeeeeee........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvs B   0 GKQLTILGSTGSIGCSTLDVVRHNPEHFRVVALVAGKNVTRmVEQCLEFSPRYAVmDDEASAKLLKTmLQQQGSRTEVLSGQQAACDmAALEDVDQVmAAIVGAAGLLPTLAAIRAGKTILLANKESLVTCGRLFmDAVKQSKAQLLPVDSEHNAIFQSLPQPIQHNLGYADLEQNGVVSILLTGSGGPFRETPLRDLATmTPDQACRHPNWSmGRKISVDSATmmNKGLEYIEARWLFNASASQmEVLIHPQSVIHSmVRYQDGSVLAQLGEPDmRTPIAHTmAWPNRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAmEAFEQGQAATTALNAANEITVAAFLAQQIRFTDIAALNLSVLEKmDmREPQCVDDVLSVDANAREVARKEVmRLAS 397
                                     9        19        29        39 |      49     |  59       |69        79       |89       |99       109       119       129     | 139       149       159       169       179       189       199|      209   |   219    || 229       239     | 249       259       269     | 279   |   289       299       309       319 |     329       339       349       359      |369       379       389   |    
                                                                    41-MSE        55-MSE      67-MSE              87-MSE    97-MSE                               135-MSE                                                          200-MSE      213-MSE    224-MSE              245-MSE      258-MSE          275-MSE 283-MSE                               321-MSE                                      366-MSE                    393-MSE
                                                                                                                                                                                                                                                           225-MSE                                                                                                                                        368-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, 6)

Asymmetric/Biological 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, 4)

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

(-) Pfam Domains  (3, 6)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  1jvs
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  DXR_ECOLI | P45568
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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_ECOLI | P45568: 1k5h 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 1JVS)