Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF (E)-4-HYDROXY-3-METHYL-BUT-2-ENYL DIPHOSPHATE REDUCTASE, THE TERMINAL ENZYME OF THE NON-MEVALONATE PATHWAY
 
Authors :  I. Rekittke
Date :  02 Jul 08  (Deposition) - 30 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trilobal Strucure, Open Alpha/Beta, Iron, Iron-Sulfur, Isoprene Biosynthesis, Metal-Binding, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Rekittke, J. Wiesner, U. Demmer, E. Warkentin, W. Xu, K. Troschke, M. Hintz, J. H. No, E. C. Duin, E. Oldfield, H. Jomaa, U. Ermler
Structure Of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, The Terminal Enzyme Of The Non-Mevalonate Pathway.
J. Am. Chem. Soc. 2008
PubMed-ID: 19035630  |  Reference-DOI: 10.1021/JA806668Q

(-) Compounds

Molecule 1 - 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.17.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-AAEOLYTB
    Expression System Strain: TOP 10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPH, LYTB, AQ_1739
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: ISPH, LYTB

 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
1F3S2Ligand/IonFE3-S4 CLUSTER
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , GLY A:15 , CYS A:96 , TYR A:98 , THR A:165 , CYS A:193 , ALA A:195BINDING SITE FOR RESIDUE F3S A 2302
2AC2SOFTWARECYS B:13 , GLY B:15 , CYS B:96 , THR B:165 , CYS B:193 , ALA B:195BINDING SITE FOR RESIDUE F3S B 3302
3AC3SOFTWAREGLY A:113 , LYS A:140 , HIS A:156 , GLU A:157 , ARG A:158BINDING SITE FOR RESIDUE GOL A 3731
4AC4SOFTWAREGLY B:113 , LYS B:140 , HIS B:156 , GLU B:157 , ARG B:158BINDING SITE FOR RESIDUE GOL B 3732

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:137
2B:107 -B:137

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DNF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DNF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DNF)

(-) Exons   (0, 0)

(no "Exon" information available for 3DNF)

(-) 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:281
 aligned with ISPH_AQUAE | O67625 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:281
                                    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 
           ISPH_AQUAE     1 MVDIIIAEHAGFCFGVKRAVKLAEESLKESQGKVYTLGPIIHNPQEVNRLKNLGVFPSQGEEFKEGDTVIIRSHGIPPEKEEALRKKGLKVIDATCPYVKAVHEAVCQLTREGYFVVLVGEKNHPEVIGTLGYLRACNGKGIVVETLEDIGEALKHERVGIVAQTTQNEEFFKEVVGEIALWVKEVKVINTICNATSLRQESVKKLAPEVDVMIIIGGKNSGNTRRLYYISKELNPNTYHIETAEELQPEWFRGVKRVGISAGASTPDWIIEQVKSRIQEI 281
               SCOP domains d3dnfa_ A: LytB                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhhhhhh......eee......hhhhhhhhhhhheee..........eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dnf A   1 MVDIIIAEHAGFCFGVKRAVKLAEESLKESQGKVYTLGPIIHNPQEVNRLKNLGVFPSQGEEFKEGDTVIIRSHGIPPEKEEALRKKGLKVIDATCPYVKAVHEAVCQLTREGYFVVLVGEKNHPEVIGTLGYLRACNGKGIVVETLEDIGEALKHERVGIVAQTTQNEEFFKEVVGEIALWVKEVKVINTICNATSLRQESVKKLAPEVDVMIIIGGKNSGNTRRLYYISKELNPNTYHIETAEELQPEWFRGVKRVGISAGASTPDWIIEQVKSRIQEI 281
                                    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 


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with ISPH_AQUAE | O67625 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:282
                                    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  
           ISPH_AQUAE     1 MVDIIIAEHAGFCFGVKRAVKLAEESLKESQGKVYTLGPIIHNPQEVNRLKNLGVFPSQGEEFKEGDTVIIRSHGIPPEKEEALRKKGLKVIDATCPYVKAVHEAVCQLTREGYFVVLVGEKNHPEVIGTLGYLRACNGKGIVVETLEDIGEALKHERVGIVAQTTQNEEFFKEVVGEIALWVKEVKVINTICNATSLRQESVKKLAPEVDVMIIIGGKNSGNTRRLYYISKELNPNTYHIETAEELQPEWFRGVKRVGISAGASTPDWIIEQVKSRIQEIC 282
               SCOP domains d3dnfb_ B: LytB                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhhhhhh......eee......hhhhhhhhhhhheee..........eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dnf B   1 MVDIIIAEHAGFCFGVKRAVKLAEESLKESQGKVYTLGPIIHNPQEVNRLKNLGVFPSQGEEFKEGDTVIIRSHGIPPEKEEALRKKGLKVIDATCPYVKAVHEAVCQLTREGYFVVLVGEKNHPEVIGTLGYLRACNGKGIVVETLEDIGEALKHERVGIVAQTTQNEEFFKEVVGEIALWVKEVKVINTICNATSLRQESVKKLAPEVDVMIIIGGKNSGNTRRLYYISKELNPNTYHIETAEELQPEWFRGVKRVGISAGASTPDWIIEQVKSRIQEIC 282
                                    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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DNF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DNF)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPH_AQUAE | O67625)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051745    4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity    Catalysis of the reaction: (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H + H+ = isopentenyl diphosphate + NAD(P)+ + H2O. Note that (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate is an alternative name for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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:0050992    dimethylallyl diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
    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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    F3S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dnf)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dnf
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ISPH_AQUAE | O67625
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.17.1.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ISPH_AQUAE | O67625
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3DNF)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DNF)