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(-) Description

Title :  CA. KORARCHAEUM CRYPTOFILUM DINUCLEOTIDE FORMING ACETYL-COENZYME A SYNTHETASE 1 IN COMPLEX WITH COENZYME A, CA-AMPCP AND HGCL+
 
Authors :  R. H. -J. Weisse, A. J. Scheidig
Date :  02 Feb 15  (Deposition) - 27 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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
 
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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric/Biological Unit (6, 21)
No.NameCountTypeFull Name
1A122Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2CA2Ligand/IonCALCIUM ION
3CL6Ligand/IonCHLORIDE ION
4COA2Ligand/IonCOENZYME A
5HG8Ligand/IonMERCURY (II) ION
6NA1Ligand/IonSODIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:46 , PRO A:47 , PRO A:59 , HG A:502binding site for residue CL A 501
02AC2SOFTWAREASN A:46 , ALA A:49 , CYS A:57 , TYR A:58 , PRO A:59 , CL A:501binding site for residue HG A 502
03AC3SOFTWARELYS A:60 , VAL A:61 , ASP A:86 , HG A:504binding site for residue CL A 503
04AC4SOFTWAREVAL A:61 , VAL A:83 , ASP A:86 , CYS A:87 , CL A:503binding site for residue HG A 504
05AC5SOFTWAREMET A:209binding site for residue HG A 505
06AC6SOFTWARELEU A:380 , TYR A:381 , GLY A:412 , VAL A:414 , PRO A:437 , HG A:507binding site for residue CL A 506
07AC7SOFTWAREALA A:310 , TYR A:381 , CYS A:382 , VAL A:414 , CL A:506 , HOH A:691binding site for residue HG A 507
08AC8SOFTWAREGLY A:17 , SER A:19 , LYS A:24 , ILE A:25 , ASN A:46 , PRO A:47 , VAL A:75 , PRO A:76 , VAL A:83 , ILE A:98 , THR A:99 , SER A:100 , ASN A:129 , ILE A:130 , HOH A:683 , HOH A:712 , HOH A:715 , HOH A:751 , HOH A:754 , HOH A:779binding site for residue COA A 508
09AC9SOFTWARELYS B:60 , VAL B:67 , LYS B:69 , SER B:70 , VAL B:75 , GLN B:111 , GLU B:112 , PHE B:113 , ALA B:114 , GLU B:119 , ASN B:211 , PRO B:212 , VAL B:223 , ASP B:224 , CA B:301 , HOH B:409 , HOH B:414 , HOH B:447 , HOH B:449 , HOH B:452binding site for residue A12 B 300
10AD1SOFTWAREASN B:211 , ASP B:224 , A12 B:300 , HOH B:409 , HOH B:412 , HOH B:413binding site for residue CA B 301
11AD2SOFTWAREASN C:46 , PRO C:47 , ALA C:49 , PRO C:59 , HG C:502binding site for residue CL C 501
12AD3SOFTWAREASN C:46 , ALA C:49 , CYS C:57 , TYR C:58 , CL C:501binding site for residue HG C 502
13AD4SOFTWAREVAL C:61 , ASP C:86 , HG C:504 , HOH C:603binding site for residue CL C 503
14AD5SOFTWAREVAL C:61 , VAL C:83 , ASP C:86 , CYS C:87 , CL C:503binding site for residue HG C 504
15AD6SOFTWAREMET C:209 , PHE C:284binding site for residue HG C 505
16AD7SOFTWARETYR C:381 , GLY C:412 , VAL C:414 , PRO C:437 , HG C:507binding site for residue CL C 506
17AD8SOFTWAREALA C:310 , TYR C:381 , CYS C:382 , CL C:506 , HOH C:640binding site for residue HG C 507
18AD9SOFTWAREMET A:355 , VAL C:16 , GLY C:17 , SER C:19 , LYS C:24 , ASN C:46 , PRO C:47 , VAL C:75 , PRO C:76 , VAL C:83 , THR C:99 , SER C:100 , HOH C:603 , HOH C:604 , HOH C:650 , HOH C:655 , HOH C:658 , HOH C:678 , HOH C:679 , HOH C:685 , HOH C:686 , HOH C:708 , HOH C:714 , HOH C:751binding site for residue COA C 508
19AE1SOFTWAREGLY D:31 , ASP D:190 , ALA D:191 , ARG D:194 , HOH D:442binding site for residue NA D 301
20AE2SOFTWARELYS D:60 , VAL D:67 , LYS D:69 , SER D:70 , VAL D:75 , GLN D:111 , GLU D:112 , PHE D:113 , ALA D:114 , GLU D:119 , ASN D:211 , PRO D:212 , VAL D:223 , ASP D:224 , CA D:303 , HOH D:417 , HOH D:433 , HOH D:436 , HOH D:440 , HOH D:446binding site for residue A12 D 302
21AE3SOFTWAREASN D:211 , ASP D:224 , A12 D:302 , HOH D:411 , HOH D:417 , HOH D:431binding site for residue CA D 303

(-) SS Bonds  (0, 0)

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

(-) 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 4XYM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XYM)

(-) 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:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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....hhhhhhhhhhhhhhhhhhhh..eee.....eeee.hhheeee.......eeeeeeee.hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xym A   1 MNDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAVR 464
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460    


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eehhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeeee......hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh....eeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xym 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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeee.......hhhhhhhhhhhhh....eeeee.....ee..ee...hhhhh.....eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhh..eee.....eeee.hhheeee.......eeeeeeee..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....hhhhhhhhhhhh..eee.hhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xym C   2 NDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLA 462
                                    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 


Chain D from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eehhhhhhhhhhh........eee.hhhhhhhhhhhhh..eeeeee......hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh....eeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xym 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)
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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 4XYM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4xz3 4y8v 4yaj 4yak 4yb8 4ybz 5hbr
        B1L7P8_KORCO | B1L7P8: 4xyl 4xz3 4y8v 4yaj 4yak 4yb8 4ybz 5hbr

(-) Related Entries Specified in the PDB File

4xyl 4XYL CONTAINS CA. KORARCHAEUM CRYPTOFILUM ACD3 IN COMPLEX WITH COENZYME A
4xz3
4y8v
4yaj
4yak
4yb8
4ybz
5hbr