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(-) Description

Title :  CRYSTAL STRUCTURE OF ISPH:INTERMEDIATE-COMPLEX
 
Authors :  M. Groll, T. Graewert, I. Span, W. Eisenreich, A. Bacher
Date :  24 Oct 09  (Deposition) - 12 Jan 10  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Fs4-Cluster Protein, All Three Domains Adopt Similar Topology, Isph:Intermediate Complex, Iron, Iron-Sulfur, Isoprene Biosynthesis, Metal-Binding, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Grawert, I. Span, W. Eisenreich, F. Rohdich, J. Eppinger, A. Bacher M. Groll
Probing The Reaction Mechanism Of Isph Protein By X-Ray Structure Analysis.
Proc. Natl. Acad. Sci. Usa V. 107 1077 2010
PubMed-ID: 20080550  |  Reference-DOI: 10.1073/PNAS.0913045107

(-) 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: PQE30
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0029, ISPH, JW0027, LYTB, YAAE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1IPE2Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , GLY A:14 , CYS A:96 , THR A:167 , CYS A:197 , IPE A:998BINDING SITE FOR RESIDUE SF4 A 997
2AC2SOFTWAREVAL A:15 , VAL A:40 , HIS A:41 , ALA A:73 , HIS A:74 , HIS A:124 , GLU A:126 , THR A:168 , ASN A:224 , SER A:225 , SER A:226 , ASN A:227 , SER A:269 , HOH A:532 , SF4 A:997BINDING SITE FOR RESIDUE IPE A 998
3AC3SOFTWARECYS B:12 , GLY B:14 , CYS B:96 , THR B:167 , CYS B:197 , IPE B:998BINDING SITE FOR RESIDUE SF4 B 997
4AC4SOFTWAREVAL B:15 , VAL B:40 , HIS B:41 , ALA B:73 , HIS B:74 , HIS B:124 , GLU B:126 , THR B:167 , THR B:168 , ASN B:224 , SER B:225 , SER B:226 , ASN B:227 , SER B:269 , HOH B:516 , SF4 B:997BINDING SITE FOR RESIDUE IPE B 998

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KE9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:7 -Pro A:8
2Ala A:31 -Pro A:32
3Asn B:7 -Pro B:8
4Ala B:31 -Pro B:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KE9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KE9)

(-) Exons   (0, 0)

(no "Exon" information available for 3KE9)

(-) 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:309
 aligned with ISPH_ECOLI | P62623 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:309
                                    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         
           ISPH_ECOLI     1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhheeee.hhhhh....eeee.....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh........eeee.hhhhhhh........eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ke9 A   1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
                                    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         


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with ISPH_ECOLI | P62623 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:310
                                    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
           ISPH_ECOLI     1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELRV 310
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --LYTB-3ke9B01 B:3-285                                                                                                                                                                                                                                                                       ------------------------- Pfam domains (1)
           Pfam domains (2) --LYTB-3ke9B02 B:3-285                                                                                                                                                                                                                                                                       ------------------------- Pfam domains (2)
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh........eeee.hhhhhhh........eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ke9 B   1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELRV 310
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3KE9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KE9)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: LYTB] (4)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ISPH_ECOLI | P62623)
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:0042380    hydroxymethylbutenyl pyrophosphate reductase activity    Catalysis of the formation of both isopentenyl pyrophosphate and dimethylallyl pyrophosphate from (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1.17.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPH_ECOLI | P62623: 3f7t 3ke8 3kef 3kel 3kem 3szl 3szo 3szu 3t0f 3t0g 3urk 3utc 3utd 3uv3 3uv6 3uv7 3uwm 3zgl 3zgn 4eb3 4h4c 4h4d 4h4e

(-) Related Entries Specified in the PDB File

3dnf ISPH CLOSED CONFORMATION
3f7t ISPH OPEN CONFORMATION
3ke8
3kef
3kel
3kem