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(-) Description

Title :  ISPH:HMBPP (SUBSTRATE) STRUCTURE OF THE E126D MUTANT
 
Authors :  I. Span, T. Graewert, A. Bacher, W. Eisenreich, M. Groll
Date :  20 Jul 11  (Deposition) - 30 Nov 11  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  3Fe-4S Iron-Sulfur Cluster, Conserved Cysteine, Ipp And Dmapp Production Final Step, Non-Mevalonate Pathway, Substrate Hmbpp, Low Activity, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Span, T. Grawert, A. Bacher, W. Eisenreich, M. Groll
Crystal Structures Of Mutant Isph Proteins Reveal A Rotatio Of The Substrate'S Hydroxymethyl Group During Catalysis.
J. Mol. Biol. V. 416 1 2012
PubMed-ID: 22137895  |  Reference-DOI: 10.1016/J.JMB.2011.11.033

(-) 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 Taxid: 562
    Gene: ISPH, LYTB, YAAE, B0029, JW0027
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ISPH

 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
1F3S2Ligand/IonFE3-S4 CLUSTER
2H6P2Ligand/Ion(2E)-4-HYDROXY-3-METHYLBUT-2-EN-1-YL TRIHYDROGENDIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1F3S1Ligand/IonFE3-S4 CLUSTER
2H6P1Ligand/Ion(2E)-4-HYDROXY-3-METHYLBUT-2-EN-1-YL TRIHYDROGENDIPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1F3S1Ligand/IonFE3-S4 CLUSTER
2H6P1Ligand/Ion(2E)-4-HYDROXY-3-METHYLBUT-2-EN-1-YL TRIHYDROGENDIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , GLY A:14 , VAL A:15 , CYS A:96 , THR A:167 , CYS A:197 , H6P A:998BINDING SITE FOR RESIDUE F3S A 317
2AC2SOFTWAREVAL A:15 , VAL A:40 , HIS A:41 , ALA A:73 , HIS A:74 , ASP A:126 , THR A:167 , THR A:168 , ASN A:224 , SER A:225 , SER A:226 , ASN A:227 , SER A:269 , F3S A:317BINDING SITE FOR RESIDUE H6P A 998
3AC3SOFTWARECYS B:12 , CYS B:96 , THR B:167 , CYS B:197 , HOH B:346 , H6P B:998BINDING SITE FOR RESIDUE F3S B 317
4AC4SOFTWAREVAL B:15 , VAL B:40 , HIS B:41 , ALA B:73 , HIS B:74 , THR B:167 , THR B:168 , ASN B:224 , SER B:225 , SER B:226 , ASN B:227 , SER B:269 , F3S B:317BINDING SITE FOR RESIDUE H6P B 998

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T0F)

(-) Cis Peptide Bonds  (5, 5)

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
5Gly B:139 -Gly B:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T0F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T0F)

(-) Exons   (0, 0)

(no "Exon" information available for 3T0F)

(-) 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:314
 aligned with ISPH_ECOLI | P62623 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:314
                                 1                                                                                                                                                                                                                                                                                                                    
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
           ISPH_ECOLI     - -----MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhheeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee.......eee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0f A  -5 HHHGSMQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPDVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
                               -1|                                                                                                                                                                                                                                                                                                                    
                                 1                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:304
 aligned with ISPH_ECOLI | P62623 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:315
                                  1                                                                                                                                                                                                                                                                                                                    
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     
           ISPH_ECOLI     - ------MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhheeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee...------.....-----..eeee.hhhhhhh........eeeee....hhhhhhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee.......eee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0f B  -6 HHHHGSMQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHA------GTMGQ-----GGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
                                 ||  4        14        24        34        44        54        64        74        84        94       104       114       | -    |   |-    |  144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304     
                                -1|                                                                                                                      122    129 133   139                                                                                                                                                                          
                                  1
   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 3T0F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T0F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T0F)

(-) 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 3ke9 3kef 3kel 3kem 3szl 3szo 3szu 3t0g 3urk 3utc 3utd 3uv3 3uv6 3uv7 3uwm 3zgl 3zgn 4eb3 4h4c 4h4d 4h4e

(-) Related Entries Specified in the PDB File

3dnf A. AEOLICUS ISPH - OPEN CONFORMATION
3f7t E. COLI ISPH - CLOSED CONFORMATION
3szl ISPH:HMBPP STRUCTURE, WILD TYPE AFTER 70 SECONDS
3szo ISPH:HMBPP STRUCTURE AFTER 3 MINUTES X-RAY PRE-EXPOSURE
3szu ISPH:HMBPP STRUCTURE, E126Q MUTANT
3t0g ISPH:HMBPP STRUCTURE, T167C MUTANT