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(-) Description

Title :  ISPH IN COMPLEX WITH 6-CHLOROPYRIDIN-3-YLMETHYL DIPHOSPHATE
 
Authors :  I. Span, K. Wang, Y. Song, W. Eisenreich, A. Bacher, E. Oldfield, M. Grol
Date :  23 Sep 13  (Deposition) - 18 Jun 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Iron-Sulfur Protein, Reductase, 6-Chloropyridin-3-Ylmethyl Diphosphate, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Span, K. Wang, W. Eisenreich, A. Bacher, Y. Zhang, E. Oldfield, M. Groll
Insights Into The Binding Of Pyridines To The Iron-Sulfur Enzyme Isph.
J. Am. Chem. Soc. V. 136 7926 2014
PubMed-ID: 24813236  |  Reference-DOI: 10.1021/JA501127J

(-) 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: XL-1 BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECDH1ME8569_0026, ISPH
    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
12E72Ligand/Ion(6-CHLOROPYRIDIN-3-YL)METHYL TRIHYDROGEN DIPHOSPHATE
2F3S2Ligand/IonFE3-S4 CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
12E71Ligand/Ion(6-CHLOROPYRIDIN-3-YL)METHYL TRIHYDROGEN DIPHOSPHATE
2F3S1Ligand/IonFE3-S4 CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12E71Ligand/Ion(6-CHLOROPYRIDIN-3-YL)METHYL TRIHYDROGEN DIPHOSPHATE
2F3S1Ligand/IonFE3-S4 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 , 2E7 A:402BINDING SITE FOR RESIDUE F3S A 401
2AC2SOFTWAREVAL A:15 , VAL A:40 , HIS A:41 , ALA A:73 , HIS A:74 , VAL A:99 , HIS A:124 , GLU 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:401BINDING SITE FOR RESIDUE 2E7 A 402
3AC3SOFTWARECYS B:12 , CYS B:96 , THR B:167 , CYS B:197 , 2E7 B:402BINDING SITE FOR RESIDUE F3S B 401
4AC4SOFTWAREVAL B:15 , VAL B:40 , HIS B:41 , HIS B:74 , VAL B:99 , 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 , F3S B:401BINDING SITE FOR RESIDUE 2E7 B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MV5)

(-) 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 4MV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MV5)

(-) Exons   (0, 0)

(no "Exon" information available for 4MV5)

(-) 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
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh........eeee.hhhhhhh........eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mv5 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
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.....ee.......eee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mv5 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)
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  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 4MV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MV5)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4MV5)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3dnf STRUCTURE OF (E)-4-HYDROXY-3-METHYL-BUT-2-ENYL DIPHOSPHATE REDUCTASE, THE TERMINAL ENZYME OF THE NON-MEVALONATE PATHWAY
3f7t STRUCTURE OF ACTIVE ISPH SHOWS A NOVEL FOLD WITH A [3FE-4S] CLUSTER IN THE CATALYTIC CENTRE
3ke8 CRYSTAL STRUCTURE OF ISPH:HMBPP-COMPLEX
4mux
4muy
4mv0