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(-) Description

Title :  ACTIVATOR OF THE 2-HYDROXYISOCAPROYL-COA DEHYDRATASE FROM CLOSTRIDIUM DIFFICILE WITH BOUND ADPNP
 
Authors :  S. H. Knauer, H. Dobbek
Date :  04 Apr 12  (Deposition) - 08 Aug 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Actin Fold, Atpase, Electron Transfer, Atp/Adp Binding, 2- Hydroxyisocaproyl-Coa Dehydratase Binding, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Knauer, W. Buckel, H. Dobbek
On The Atp-Dependent Activation Of The Radical Enzyme (R)-2-Hydroxyisocaproyl-Coa Dehydratase.
Biochemistry V. 51 6609 2012
PubMed-ID: 22827463  |  Reference-DOI: 10.1021/BI300571Z

(-) Compounds

Molecule 1 - ACTIVATOR OF 2-HYDROXYISOCAPROYL-COA DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) CODONPLUS-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HADI
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 1496

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG2Ligand/IonMAGNESIUM ION
4NA3Ligand/IonSODIUM ION
5SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:125 , ALA A:126 , CYS A:164 , THR A:165 , CYS B:125 , ALA B:126 , ALA B:127 , CYS B:164 , THR B:165BINDING SITE FOR RESIDUE SF4 A 301
02AC2SOFTWAREGLY A:9 , SER A:10 , THR A:11 , ALA A:12 , LYS A:14 , GLY A:101 , GLY A:102 , GLN A:103 , ASP A:104 , GLY A:130 , ASP A:134 , VAL A:144 , SER A:145 , GLY A:214 , GLY A:215 , VAL A:216 , ARG A:218 , ASN A:219 , GLN A:241 , MG A:303 , NA A:305 , HOH A:403 , HOH A:422 , HOH A:487 , HOH A:511 , HOH A:531 , HOH A:532 , HOH A:533 , HOH A:534 , HOH A:536 , HOH A:537 , HOH A:538 , HOH A:615 , HOH A:649BINDING SITE FOR RESIDUE ANP A 302
03AC3SOFTWAREANP A:302 , HOH A:531 , HOH A:532 , HOH A:533 , HOH A:534BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWAREILE A:140 , LEU A:176 , HOH A:654BINDING SITE FOR RESIDUE ACT A 304
05AC5SOFTWAREALA A:12 , SER A:31 , GLN A:241 , ANP A:302BINDING SITE FOR RESIDUE NA A 305
06AC6SOFTWAREILE A:239 , PRO A:240 , GLN A:241 , HOH A:524BINDING SITE FOR RESIDUE NA A 306
07AC7SOFTWARESER A:151 , ARG A:224 , HOH A:428 , HOH A:442BINDING SITE FOR RESIDUE ACT A 307
08AC8SOFTWAREGLY B:9 , SER B:10 , THR B:11 , ALA B:12 , LYS B:14 , GLY B:101 , GLY B:102 , GLN B:103 , ASP B:104 , GLY B:130 , ASP B:134 , VAL B:144 , SER B:145 , GLY B:214 , GLY B:215 , VAL B:216 , ARG B:218 , GLN B:241 , MG B:302 , HOH B:402 , HOH B:404 , HOH B:406 , HOH B:408 , HOH B:450 , HOH B:465 , HOH B:474 , HOH B:475 , HOH B:476 , HOH B:480BINDING SITE FOR RESIDUE ANP B 301
09AC9SOFTWAREANP B:301 , HOH B:474 , HOH B:475 , HOH B:476 , HOH B:477BINDING SITE FOR RESIDUE MG B 302
10BC1SOFTWAREARG B:131 , HOH B:490BINDING SITE FOR RESIDUE ACT B 303
11BC2SOFTWAREILE B:239 , PRO B:240 , GLN B:241 , HOH B:407BINDING SITE FOR RESIDUE NA B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:208 -Asn A:209
2Arg B:208 -Asn B:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EHU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EHU)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee...eeeeeeee......hhhhhhhhhhhhhhh.hhh.eeeeeee..hhhhh....ee.hhhhhhhhhhhhhh....eeeee....eeeeee.....eeeeeee......hhhhhhhhhhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ehu A   1 MYTMGLDIGSTASKGVILKNGEDIVASETISSGTGTTGPSRVLEKLYGKTGLAREDIKKVVVTGYGRMNYSDADKQISELSCHARGVNFIIPETRTIIDIGGQDAKVLKLDNNGRLLNFLMNDKCAAGTGRFLDVMAKIIEVDVSELGSISMNSQNEVSISSTCTVFAESEVISHLSENAKIEDIVAGIHTSVAKRVSSLVKRIGVQRNVVMVGGVARNSGIVRAMAREINTEIIVPDIPQLTGALGAALYAFDEAKESQKEVKNISA 268
                                    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        


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee...eeeeeeee......hhhhhhhhhhhhhhh.hhhhh.eeeee..hhhhh....ee.hhhhhhhhhhhhhh....eeeee....eeeeee.....eeeeeee......hhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ehu B   1 MYTMGLDIGSTASKGVILKNGEDIVASETISSGTGTTGPSRVLEKLYGKTGLAREDIKKVVVTGYGRMNYSDADKQISELSCHARGVNFIIPETRTIIDIGGQDAKVLKLDNNGRLLNFLMNDKCAAGTGRFLDVMAKIIEVDVSELGSISMNSQNEVSISSTCTVFAESEVISHLSENAKIEDIVAGIHTSVAKRVSSLVKRIGVQRNVVMVGGVARNSGIVRAMAREINTEIIVPDIPQLTGALGAALYAFDEAKES 259
                                    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
   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 4EHU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:208 - Asn A:209   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        HADI_CLODI | Q5U925: 4eht 4eia

(-) Related Entries Specified in the PDB File

4eht ACTIVATOR OF THE 2-HYDROXYISOCAPROYL-COA DEHYDRATASE FROM CLOSTRIDIUM DIFFICILE WITH BOUND ADP
4eia ACTIVATOR OF THE 2-HYDROXYISOCAPROYL-COA DEHYDRATASE FROM CLOSTRIDIUM DIFFICILE WITHOUT NUCLEOTIDE