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(-) Description

Title :  CA. KORARCHAEUM CRYPTOFILUM DINUCLEOTIDE FORMING ACETYL-COENZYME A SYNTHETASE 1 (APO FORM)
 
Authors :  R. H. -J. Weisse, A. J. Scheidig
Date :  17 Feb 15  (Deposition) - 27 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dinucleotide Forming Acetyl-Coa Synthetase, Complex, Acd, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. H. Weie, A. Faust, M. Schmidt, P. Schonheit, A. J. Scheidig
Structure Of Ndp-Forming Acetyl-Coa Synthetase Acd1 Reveals A Large Rearrangement For Phosphoryl Transfer.
Proc. Natl. Acad. Sci. Usa V. 113 E519 2016
PubMed-ID: 26787904  |  Reference-DOI: 10.1073/PNAS.1518614113

(-) Compounds

Molecule 1 - ALPHA SUBUNIT OF ACETYL-COENZYME A SYNTHETASE (DINUCLEOTIDE-FORMING) 3
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: KCR_0198
    Organism Scientific: KORARCHAEUM CRYPTOFILUM OPF8
    Organism Taxid: 374847
 
Molecule 2 - BETA SUBUNIT OF ACETYL-COENZYME A SYNTHETASE (DINUCLEOTIDE- FORMING) 3
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KCR_0115
    Organism Scientific: KORARCHAEUM CRYPTOFILUM OPF8
    Organism Taxid: 374847

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:51 , MET A:53 , GLY A:54 , GLU B:12binding site for residue NA A 501
2AC2SOFTWARELEU B:6 , LYS B:9 , ALA B:10 , ARG B:15 , GLU B:22binding site for residue NA B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Gly A:127 -Pro A:128
2Asn A:348 -Pro A:349
3Phe B:55 -Pro B:56
4Ala B:154 -Pro B:155
5Asn B:211 -Pro B:212
6Gly C:127 -Pro C:128
7Asn C:348 -Pro C:349
8Phe D:55 -Pro D:56
9Ala D:154 -Pro D:155
10Asn D:211 -Pro D:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAJ)

(-) 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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee.......hhhhhhhhhhhhh....eeeee.....ee..ee...hhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eee.....eeee.hhheeee.......eeeeeeee..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhhh........hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yaj A   3 DLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAV 463
                                    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 


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeeee............eeeee.hhhhhhhhhhhhhhhhhh........eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh...eeeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yaj B   2 SSRDLLLKAKENGRKSLLEHEAKYFISSYGIPVTNIRLAKSEEEAVNFSREIGFPVVLKIVSPQVVHKSDVGGVKVNLRSEEEVRKAYREIIENVKRNVPNAEIEGILVQEFAPPGVELIIGLLRDPQFGPTVMFGLGGVFVELFRDVSFRVAPLSEQDAESMIKEVKAYKLLTGFRGMEPVDIEAIKDALIRAGRIGVENEEIAEMDLNPVIAYPKGIKVVDARIILR 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         


Chain C from PDB  Type:PROTEIN  Length:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee.......hhhhhhhhhhhhhh...eeeee.....ee..ee...hhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eee.....eeee.hhheeee.......eeeeeeee..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhh......hhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yaj C   3 DLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAASSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAV 463
                                    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||     265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455        
                                                                                                                                                                                                                                                                                    253|                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                     257                                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhh...eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh....eeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yaj D   2 SSRDLLLKAKENGRKSLLEHEAKYFISSYGIPVTNIRLAKSEEEAVNFSREIGFPVVLKIVSPQVNLRSEEEVRKAYREIIENEIEGILVQEFAPPGVELIIGLLRDPQFGPTVMFGLGGVFVELFRDVSFRVAPLSEQDAESMIKEVKAYKLLTGFRGMEPVDIEAIKDALIRAGRIGVENEEIAEMDLNPVIAYPKGIKVVDARIILR 230
                                    11        21        31        41        51        61   ||   82        92  ||   110       120       130       140       150       160       170       180       190       200       210       220       230
                                                                                          65|                95|                                                                                                                              
                                                                                           77                104
   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 4YAJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:154 - Pro B:155   [ RasMol ]  
    Ala D:154 - Pro D:155   [ RasMol ]  
    Asn A:348 - Pro A:349   [ RasMol ]  
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    Gly A:127 - Pro A:128   [ RasMol ]  
    Gly C:127 - Pro C:128   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        B1L3C9_KORCO | B1L3C9: 4xyl 4xym 4xz3 4y8v 4yak 4yb8 4ybz 5hbr
        B1L7P8_KORCO | B1L7P8: 4xyl 4xym 4xz3 4y8v 4yak 4yb8 4ybz 5hbr

(-) Related Entries Specified in the PDB File

4xyl 4xym 4xz3 4y8v 4yak 4yb8 4ybz 5hbr