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(-) Description

Title :  ACTIVATOR OF THE 2-HYDROXYISOCAPROYL-COA DEHYDRATASE FROM CLOSTRIDIUM DIFFICILE WITH BOUND ADP
 
Authors :  S. H. Knauer, H. Dobbek
Date :  04 Apr 12  (Deposition) - 08 Aug 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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  (6, 11)

Asymmetric/Biological Unit (6, 11)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CL2Ligand/IonCHLORIDE ION
4MG2Ligand/IonMAGNESIUM ION
5NH41Ligand/IonAMMONIUM ION
6SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:125 , CYS A:164 , THR A:165 , CYS B:125 , 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 , GLY A:130 , ASP A:134 , VAL A:144 , SER A:145 , GLY A:214 , GLY A:215 , VAL A:216 , ARG A:218 , GLN A:241 , MG A:303 , CL A:307 , HOH A:423 , HOH A:429 , HOH A:442 , HOH A:449 , HOH A:463 , HOH A:466 , HOH A:476 , HOH A:505 , HOH A:509 , HOH A:522BINDING SITE FOR RESIDUE ADP A 302
03AC3SOFTWAREADP A:302 , HOH A:462 , HOH A:463 , HOH A:465 , HOH A:521 , HOH A:522BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWARESER A:151 , ARG A:224 , HOH A:433 , HOH A:479BINDING SITE FOR RESIDUE ACT A 304
05AC5SOFTWARESER A:81 , GLY A:114 , ARG A:115 , LEU A:116 , HOH A:483BINDING SITE FOR RESIDUE ACT A 305
06AC6SOFTWAREILE A:239 , PRO A:240 , GLN A:241 , HOH A:428BINDING SITE FOR RESIDUE CL A 306
07AC7SOFTWAREALA A:12 , SER A:31 , GLN A:241 , ADP A:302BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREGLY B:9 , SER B:10 , THR B:11 , ALA B:12 , LYS B:14 , GLY B:101 , GLY B:102 , GLY B:130 , ASP B:134 , SER B:145 , GLY B:214 , GLY B:215 , VAL B:216 , ARG B:218 , GLN B:241 , MG B:302 , NH4 B:304 , HOH B:414 , HOH B:430 , HOH B:431 , HOH B:432 , HOH B:440 , HOH B:441 , HOH B:442 , HOH B:475BINDING SITE FOR RESIDUE ADP B 301
09AC9SOFTWAREADP B:301 , HOH B:429 , HOH B:430 , HOH B:473 , HOH B:474 , HOH B:475BINDING SITE FOR RESIDUE MG B 302
10BC1SOFTWAREILE B:239 , PRO B:240 , GLN B:241 , LEU B:242BINDING SITE FOR RESIDUE ACT B 303
11BC2SOFTWAREALA B:12 , SER B:31 , GLN B:241 , ADP B:301BINDING SITE FOR RESIDUE NH4 B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr A:34 -Gly A:35
2Ser A:71 -Asp A:72
3Arg A:208 -Asn A:209
4Ser B:71 -Asp B:72
5Arg B:208 -Asn B:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EHT)

(-) 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...........ee.hhhhhhhhhhhhhh....eeeee....eeeeee.....eeeeeee......hhhhhhhhhhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eht 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee...eeeeeeee......hhhhhhhhhhhhhhh.hhhhh.eeeee...........ee.hhhhhhhhhhhhhh....eeeee....eeeeee.....eeeeeee......hhhhhhhhhhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eht B   1 MYTMGLDIGSTASKGVILKNGEDIVASETISSGTGTTGPSRVLEKLYGKTGLAREDIKKVVVTGYGRMNYSDADKQISELSCHARGVNFIIPETRTIIDIGGQDAKVLKLDNNGRLLNFLMNDKCAAGTGRFLDVMAKIIEVDVSELGSISMNSQNEVSISSTCTVFAESEVISHLSENAKIEDIVAGIHTSVAKRVSSLVKRIGVQRNVVMVGGVARNSGIVRAMAREINTEIIVPDIPQLTGALGAALYAFDEAKESQ 260
                                    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
   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 4EHT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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    Ser A:71 - Asp A:72   [ RasMol ]  
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    Thr A:34 - Gly A:35   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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