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(-) Description

Title :  SUCCINYL-COA:ACETATE COA-TRANSFERASE (AARCH6) BOUND TO ACETATE AND THE COA ANALOGUE 3'-PHOSPHOADENOSINE 5'-(O-(N-PROPYL-R-PANTOTHENAMIDE)) PYROPHOSPHATE (MX)
 
Authors :  T. J. Kappock, J. R. Murphy
Date :  22 Sep 15  (Deposition) - 04 May 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tricarboxylic Acid Cycle, Transferase, Acidophile, Coenzyme Analogue (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Murphy, E. A. Mullins, T. J. Kappock
Functional Dissection Of The Bipartite Active Site Of The Class I Coenzyme A (Coa)-Transferase Succinyl-Coa:Acetate Coa-Transferase.
Front Chem V. 4 23 2016
PubMed-ID: 27242998  |  Reference-DOI: 10.3389/FCHEM.2016.00023
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Chains: A, B
    EC Number: 2.8.3.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AZ09_02565
    Organism Scientific: ACETOBACTER ACETI 1023
    Organism Taxid: 1457393

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
10T12Ligand/Ion[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(3R)-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-4-[[3-OXIDANYLIDENE-3-(PROPYLAMINO)PROPYL]AMINO]BUTYL]HYDROGEN PHOSPHATE
2ACT6Ligand/IonACETATE ION
3IMD3Ligand/IonIMIDAZOLE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:36 , SER A:71 , PHE A:92 , THR A:94 , ARG A:228 , VAL A:270 , HOH A:877binding site for residue ACT A 601
02AC2SOFTWAREGLN A:267 , GLU A:294 , ASN A:361 , GLY A:362 , MET A:363 , ILE A:364 , SER A:374 , ASN A:384 , GLY A:385 , ILE A:386 , GLY A:388 , SER A:389 , ALA A:407 , LYS A:408 , ILE A:412 , HOH A:707 , HOH A:741 , HOH A:758 , HOH A:760 , HOH A:763 , HOH A:794 , HOH A:798 , HOH A:801 , HOH A:808 , HOH A:829 , HOH A:831 , HOH A:843 , HOH A:866 , HOH A:921 , HOH A:923 , HOH A:964 , HOH A:994 , HOH A:1006 , HOH A:1051 , LYS B:240binding site for residue 0T1 A 602
03AC3SOFTWARETHR A:487 , LEU A:490 , SER A:491 , GLN A:494 , HOH A:927 , LEU B:486binding site for residue IMD A 603
04AC4SOFTWAREMET A:418 , ALA A:419 , ALA B:419binding site for residue IMD A 604
05AC5SOFTWAREARG A:354 , HOH A:835 , HOH A:965 , VAL B:196 , SER B:348 , ARG B:354binding site for residue ACT A 605
06AC6SOFTWAREPHE A:110 , ASN A:112 , ARG A:120 , ASN A:125 , HOH A:1055 , ARG B:442 , GLY B:443binding site for residue ACT A 606
07AC7SOFTWAREVAL A:196 , ARG A:354 , HOH A:904 , ARG B:354 , HOH B:821binding site for residue ACT B 601
08AC8SOFTWAREARG A:442 , GLY A:443 , ASN B:112 , ARG B:120 , ASN B:125binding site for residue ACT B 602
09AC9SOFTWARETHR B:36 , SER B:71 , THR B:94 , ASN B:229 , HOH B:853binding site for residue ACT B 603
10AD1SOFTWAREGLN B:267 , VAL B:270 , GLY B:271 , ASN B:272 , VAL B:273 , GLU B:294 , ASN B:361 , GLY B:362 , MET B:363 , ILE B:364 , ASN B:384 , GLY B:385 , ILE B:386 , GLY B:388 , SER B:389 , ALA B:407 , LYS B:408 , ILE B:412 , HOH B:713 , HOH B:727 , HOH B:735 , HOH B:752 , HOH B:758 , HOH B:789 , HOH B:826 , HOH B:827 , HOH B:841 , HOH B:843 , HOH B:877 , HOH B:894 , HOH B:910 , HOH B:973 , HOH B:977 , HOH B:999 , HOH B:1014binding site for residue 0T1 B 604
11AD2SOFTWARELEU A:486 , THR B:487 , LEU B:490 , SER B:491 , GLN B:494 , HOH B:907 , HOH B:1129binding site for residue IMD B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DW6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:90 -Pro A:91
2Pro A:191 -Thr A:192
3Ser B:90 -Pro B:91
4Pro B:191 -Thr B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DW6)

(-) Exons   (0, 0)

(no "Exon" information available for 5DW6)

(-) 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:512
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.hhhhhhh......eeee.........hhhhhhhhhhhhhhhhh.....eeee........hhhhhhhh..eeeee....hhhhhhhhhh...ee...hhhhhhhhhhhh......eeeeeeeee.....eee.....hhhhhhhhh.eeeeeee...hhhhh..ee...............................hhh.eeeeeee............hhhhhhhhhhhhhhhhhhhhh.........ee...hhhhhhhhhhhhhh....eeee..eeehhhhhhhhhh.eeeeee.eee.hhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh.eeee...eee....ee..eehhhee.....hhhhhhhhh.eeeee...ee....ee.ee........hhhhh.eeee..eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh............hhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dw6 A   3 ERIRNVALRSKVCPAETASELIKHGDVVGTSGFTGAGYPKEVPKALAQRMEAAHDRGEKYQISLITGASTGPQLDGELAKANGVYFRSPFNTDATMRNRINAGETEYFDNHLGQVAGRAVQGNYGKFNIALVEATAITEDGGIVPTSSVGNSQTFLNLAEKVIIEVNEWQNPMLEGIHDIWDGNVSGVPTRDIVPIVRADQRVGGPVLRVNPDKIAAIVRTNDRDRNAPFAAPDETAKAIAGYLLDFFGHEVKQNRLPPSLLPLQSGVGNVANAVLEGLKEGPFENLVGYSEVIQDGMLAMLDSGRMRIASASSFSLSPEAAEEINNRMDFFRSKIILRQQDVSNSPGIIRRLGCIAMNGMIEADIYGNVNSTRVMGSKMMNGIGGSGDFARSSYLSIFLSPSTAKGGKISAIVPMAAHVDHIMQDAQIFVTEQGLADLRGLSPVQRAREIISKCAHPDYRPMLQDYFDRALKNSFGKHTPHLLTEALSWHQRFIDTGTMLPSSLEHHHHHH 514
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512  


Chain B from PDB  Type:PROTEIN  Length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhh.hhhhhhh......eeee.........hhhhhhhhhhhhhhhhh.....eeee........hhhhhhhh..eeeee....hhhhhhhhhh...ee...hhhhhhhhhhhh......eeeeee.ee.....ee......hhhhhhhhh.eeeeeee...hhhhh..ee...............................hhh.eeeeeee............hhhhhhhhhhhhhhhhhhhhh.........eee..hhhhhhhhhhhh......eeee..eeehhhhhhhhhh.eeeeee.eee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh.eeeee..eee....ee..eehhhee.....hhhhhhhhh.eeeee...eehhhhee.ee........hhhhh.eeee..eeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh............hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dw6 B   2 TERIRNVALRSKVCPAETASELIKHGDVVGTSGFTGAGYPKEVPKALAQRMEAAHDRGEKYQISLITGASTGPQLDGELAKANGVYFRSPFNTDATMRNRINAGETEYFDNHLGQVAGRAVQGNYGKFNIALVEATAITEDGGIVPTSSVGNSQTFLNLAEKVIIEVNEWQNPMLEGIHDIWDGNVSGVPTRDIVPIVRADQRVGGPVLRVNPDKIAAIVRTNDRDRNAPFAAPDETAKAIAGYLLDFFGHEVKQNRLPPSLLPLQSGVGNVANAVLEGLKEGPFENLVGYSEVIQDGMLAMLDSGRMRIASASSFSLSPEAAEEINNRMDFFRSKIILRQQDVSNSPGIIRRLGCIAMNGMIEADIYGNVNSTRVMGSKMMNGIGGSGDFARSSYLSIFLSPSTAKGGKISAIVPMAAHVDHIMQDAQIFVTEQGLADLRGLSPVQRAREIISKCAHPDYRPMLQDYFDRALKNSFGKHTPHLLTEALSWHQRFIDTGTMLPS 505
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
   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 5DW6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DW6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DW6)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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    Pro A:191 - Thr A:192   [ RasMol ]  
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  2.8.3.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        SCACT_ACEAC | B3EY95: 4eu3 4eu4 4eu5 4eu6 4eu7 4eu8 4eu9 4eua 4eub 4euc 4eud 5ddk 5dw4 5dw5 5e5h

(-) Related Entries Specified in the PDB File

4fac SAME PROTEIN BOUND TO DETHIAACETYL-COA (ACMX) DERIVED ACETATE AND COA ANALOGUE, WITH ONE ACETYLGLUTAMYL ANHYDRIDE ADDUCT.
5dw4
5dw5