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(-) Description

Title :  CA. KORARCHAEUM CRYPTOFILUM DINUCLEOTIDE FORMING ACETYL-COENZYME A SYNTHETASE 1 IN COMPLEX WITH ADP AND WITH PHOSPHORYLATED PHOSPHOHISTIDINE SEGMENT (SITE I ORIENTATION)
 
Authors :  R. H. -J. Weisse, A. J. Scheidig
Date :  19 Feb 15  (Deposition) - 27 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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 ACYL-COA SYNTHETASE (NDP FORMING)
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: KCR_0198
    Organism Scientific: KORARCHAEUM CRYPTOFILUM (STRAIN OPF8)
    Organism Taxid: 374847
    Other Details: PHOSPHORYLATED HIS254
    Strain: OPF8
 
Molecule 2 - BETA SUBUNIT OF ACYL-COA SYNTHETASE (NDP FORMING)
    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 (STRAIN OPF8)
    Organism Taxid: 374847
    Strain: OPF8

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3NEP2Mod. Amino AcidN1-PHOSPHONOHISTIDINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENEP A:254 , ASP C:351binding site for residue MG A 501
2AC2SOFTWAREHOH A:685 , HOH A:686 , HOH A:793 , NEP C:254 , HOH C:715binding site for residue MG C 501
3AC3SOFTWAREVAL D:58 , LYS D:60 , HIS D:68 , LYS D:69 , SER D:70 , GLN D:111 , GLU D:112 , PHE D:113 , ALA D:114 , VAL D:223 , ASP D:224 , ARG D:226 , HOH D:439 , HOH D:441 , HOH D:442 , HOH D:443binding site for residue ADP D 300

(-) SS Bonds  (0, 0)

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

(-) 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 4YBZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBZ)

(-) 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:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               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...hhhhhhhhhhhhh....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
                 4ybz A   2 NDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAAShTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAVR 464
                                    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   
                                                                                                                                                                                                                                                                                      254-NEP                                                                                                                                                                                                              


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......hhhhh.eeeee...hhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh....eeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybz 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:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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.......hhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....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
                 4ybz C   3 DLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAAShTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAVR 464
                                    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  
                                                                                                                                                                                                                                                                                     254-NEP                                                                                                                                                                                                              


Chain D 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......hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybz D   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
   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 4YBZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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