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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REDUCTOISOMERASE COMPLEXED WITH A BISPHOSPHONATE
 
Authors :  S. Yajima, K. Hara, J. M. Sanders, F. Yin, K. Ohsawa, J. Wiesner, H. Jomaa, E. Oldfield
Date :  17 Apr 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Three Domains, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yajima, K. Hara, J. M. Sanders, F. Yin, K. Ohsawa, J. Wiesner, H. Jomaa, E. Oldfield
Crystallographic Structures Of Two Bisphosphonate:1-Deoxyxylulose-5-Phosphate Reductoisomerase Complexes
J. Am. Chem. Soc. V. 126 10824 2004
PubMed-ID: 15339150  |  Reference-DOI: 10.1021/JA040126M
(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 Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE REDUCTOISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1IMB2Ligand/Ion[(ISOQUINOLIN-1-YLAMINO)-PHOSPHONO-METHYL]-PHOSPHONICACID
2SO42Ligand/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 , IMB A:3001BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREGLY B:184 , SER B:185 , HIS B:208 , SER B:221 , ASN B:226 , LYS B:227 , IMB B:2001BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWARELYS B:124 , ASP B:149 , SER B:150 , GLU B:151 , TRP B:211 , MET B:213 , ASN B:226 , LYS B:227 , GLU B:230 , PRO B:273 , MET B:275 , SO4 B:1002BINDING SITE FOR RESIDUE IMB B 2001
4AC4SOFTWARELYS A:124 , ASP A:149 , SER A:150 , GLU A:151 , TRP A:211 , MET A:213 , ASN A:226 , GLU A:230 , PRO A:273 , MET A:275 , SO4 A:1001BINDING SITE FOR RESIDUE IMB A 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T1R)

(-) 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 1T1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T1R)

(-) Exons   (0, 0)

(no "Exon" information available for 1T1R)

(-) 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: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 -d1t1ra2 A:1-125 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                              d1t1ra4 A:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1t1ra3 A:275-300         d1t1ra1 A:301-397 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain              SCOP domains
               CATH domains 1t1rA01 A:0-149 NAD(P)-binding Rossmann-like Domain                                                                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------1t1rA03 A:311-397  [code=1.10.1740.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhhh.....eeee......hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhh.hhhhhh...........eeeeeeee........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t1r A   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        


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 -d1t1rb2 B:1-125 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                              d1t1rb4 B:126-274 1-deoxy-D-xylulose-5-phosphate reductoisomerase                                                                                    d1t1rb3 B:275-300         d1t1rb1 B:301-397 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain              SCOP domains
               CATH domains 1t1rB01 B:0-149 NAD(P)-binding Rossmann-like Domain                                                                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------1t1rB03 B:311-397  [code=1.10.1740.10, no name defined]                                 CATH domains
           Pfam domains (1) ---DXP_reductoisom-1t1rB03 B:3-131                                                                                                  -------------DXP_redisom_C-1t1rB01 B:145-238                                                               -------------------------------DXPR_C-1t1rB05 B:270-388                                                                                               --------- Pfam domains (1)
           Pfam domains (2) ---DXP_reductoisom-1t1rB04 B:3-131                                                                                                  -------------DXP_redisom_C-1t1rB02 B:145-238                                                               -------------------------------DXPR_C-1t1rB06 B:270-388                                                                                               --------- Pfam domains (2)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhh......eeee...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh......hhhh.eeeeeeee........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t1r 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
   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, 8)

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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  1t1r
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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: 1jvs 1k5h 1onn 1ono 1onp 1q0h 1q0l 1q0q 1t1s 2egh 3anl 3anm 3ann 3r0i

(-) Related Entries Specified in the PDB File

1jvs THE SAME PEOTEIN WITHOUT A BISPHOSPHONATE
1t1s THE SAME PROTEIN WITH ANOTHER BISPHOSHONATE