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(-) Description

Title :  TYPE III POLYKETIDE SYNTHASE
 
Authors :  T. Mori, Y. Shimokawa, T. Matsui, R. Kato, S. Sugio, H. Morita, I. Abe
Date :  10 Jun 13  (Deposition) - 04 Sep 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acridone Synthase, Type Iii Polyketide Synthase, Acyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Mori, Y. Shimokawa, T. Matsui, K. Kinjo, R. Kato, H. Noguchi, S. Sugio, H. Morita, I. Abe
Cloning, Characterization, And Crystal Structure Analysis O Novel Type Iii Polyketide Synthases From Citrus Microcarpa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TYPE III POLYKETIDE SYNTHASES ACRIDONE SYNTHASE
    Chains: A, B
    EC Number: 2.3.1.159
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE80L
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: CALAMONDIN
    Organism Scientific: CITRUS MICROCARPA
    Organism Taxid: 164113

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2NI9Ligand/IonNICKEL (II) ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:59 , LYS A:62 , CYS A:164 , ASP A:207 , VAL A:210 , LEU A:267 , LYS A:268 , LYS A:269 , VAL A:271 , GLY A:305 , GLY A:306 , PRO A:307 , ALA A:308 , HOH A:603 , HOH A:648 , HOH A:652 , HOH A:682BINDING SITE FOR RESIDUE COA A 401
02AC2SOFTWAREHIS A:205 , ASP A:207 , HIS A:266 , HOH A:635 , HOH A:643BINDING SITE FOR RESIDUE NI A 402
03AC3SOFTWAREHIS A:329 , GLU A:333 , HOH A:580 , HOH A:602 , HOH A:666BINDING SITE FOR RESIDUE NI A 403
04AC4SOFTWAREHIS A:-2 , HOH A:568 , HOH A:609 , HIS B:-4 , HIS B:-6 , GLU B:5BINDING SITE FOR RESIDUE NI A 404
05AC5SOFTWAREHIS A:-3 , HIS B:-5 , HIS B:-7 , MET B:-11BINDING SITE FOR RESIDUE NI A 405
06AC6SOFTWAREHIS A:-7 , MET A:-11 , HOH A:675 , HIS B:-2BINDING SITE FOR RESIDUE NI A 406
07AC7SOFTWAREHIS A:-5 , HOH A:553 , HOH A:627 , HOH A:669 , HIS B:-3BINDING SITE FOR RESIDUE NI A 407
08AC8SOFTWAREHIS A:-6 , HIS A:-4 , HOH A:594 , HOH A:668BINDING SITE FOR RESIDUE NI A 408
09AC9SOFTWAREHIS A:-3 , HIS A:-4BINDING SITE FOR RESIDUE SO4 A 409
10BC1SOFTWARELYS B:55 , LEU B:59 , LYS B:62 , ASP B:207 , VAL B:210 , LEU B:267 , LYS B:268 , VAL B:271 , GLY B:306 , PRO B:307 , ALA B:308 , PHE B:373 , HOH B:649BINDING SITE FOR RESIDUE COA B 401
11BC2SOFTWAREHIS B:329 , GLU B:333 , HOH B:604 , HOH B:616 , HOH B:638BINDING SITE FOR RESIDUE NI B 402
12BC3SOFTWAREHIS B:205 , ASP B:207 , HIS B:266 , HOH B:532 , HOH B:565BINDING SITE FOR RESIDUE NI B 403
13BC4SOFTWAREHOH A:553 , HIS B:-6 , HIS B:-5BINDING SITE FOR RESIDUE SO4 B 404
14BC5SOFTWAREHIS B:-3 , HIS B:-2 , HIS B:-4 , MET B:1 , HOH B:555 , HOH B:634BINDING SITE FOR RESIDUE SO4 B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WD7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Met A:137 -Pro A:138
2Gly A:376 -Leu A:377
3Met B:137 -Pro B:138
4Gly B:376 -Leu B:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WD7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WD7)

(-) Exons   (0, 0)

(no "Exon" information available for 3WD7)

(-) 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:401
 aligned with U3KRF0_9ROSI | U3KRF0 from UniProtKB/TrEMBL  Length:391

    Alignment length:401
                                        1                                                                                                                                                                                                                                                                                                                                                                                                    
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388 
         U3KRF0_9ROSI     - ------------MVTMEEIRRAKRAEGLATILAISTATPPNCVIQADYPDYYFGITNSEHMTELKEKFKLLCEKSMIRKRHMCLTEEILKANPNMCLYMGTSLDARQDISLVEVPKLGKEAATKAIKEWGQPKSNITHLIFCTSAGVDMPGADYQLTRLIGLNPDVKRMMIYQQGCYAGATILRLAKDLAENNKGSRVLVVCSENTIPTFRGPSYTHIDSLVGQALFADGAAALIVGADPDTSIERPLYHIVSASQTLLPDSDGAIEGHIREAGLTVHLKKDVPEFFSANIEKSLVDAFTPIGISDWNSIFWIAHPGGPAILDQVEAKLGLKKDKLRASRHVMSEYGNMSSACVLFILDEMRNKCLEEGKATTGEGLDWGVLFGFGPGLTVETVVLHSLPI 389
               SCOP domains d3wd7a1 A:-11-235 automated matches                                                                                                                                                                                                                    d3wd7a2 A:236-389 automated matches                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhh.....eeeeeeee....eee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....ee.hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee............hhhhhhhhhhh..eeeeeeee...........eeeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..........eeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wd7 A -11 MRGSHHHHHHGSMVTMEEIRRAKRAEGLATILAISTATPPNCVIQADYPDYYFGITNSEHMTELKEKFKLLCEKSMIRKRHMCLTEEILKANPNMCLYMGTSLDARQDISLVEVPKLGKEAATKAIKEWGQPKSNITHLIFCTSAGVDMPGADYQLTRLIGLNPDVKRMMIYQQGCYAGATILRLAKDLAENNKGSRVLVVCSENTIPTFRGPSYTHIDSLVGQALFADGAAALIVGADPDTSIERPLYHIVSASQTLLPDSDGAIEGHIREAGLTVHLKKDVPEFFSANIEKSLVDAFTPIGISDWNSIFWIAHPGGPAILDQVEAKLGLKKDKLRASRHVMSEYGNMSSACVLFILDEMRNKCLEEGKATTGEGLDWGVLFGFGPGLTVETVVLHSLPI 389
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388 


Chain B from PDB  Type:PROTEIN  Length:401
 aligned with U3KRF0_9ROSI | U3KRF0 from UniProtKB/TrEMBL  Length:391

    Alignment length:401
                                        1                                                                                                                                                                                                                                                                                                                                                                                                    
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388 
         U3KRF0_9ROSI     - ------------MVTMEEIRRAKRAEGLATILAISTATPPNCVIQADYPDYYFGITNSEHMTELKEKFKLLCEKSMIRKRHMCLTEEILKANPNMCLYMGTSLDARQDISLVEVPKLGKEAATKAIKEWGQPKSNITHLIFCTSAGVDMPGADYQLTRLIGLNPDVKRMMIYQQGCYAGATILRLAKDLAENNKGSRVLVVCSENTIPTFRGPSYTHIDSLVGQALFADGAAALIVGADPDTSIERPLYHIVSASQTLLPDSDGAIEGHIREAGLTVHLKKDVPEFFSANIEKSLVDAFTPIGISDWNSIFWIAHPGGPAILDQVEAKLGLKKDKLRASRHVMSEYGNMSSACVLFILDEMRNKCLEEGKATTGEGLDWGVLFGFGPGLTVETVVLHSLPI 389
               SCOP domains d3wd7b1 B:-11-235 automated matches                                                                                                                                                                                                                    d3wd7b2 B:236-389 automated matches                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh.....eeeeeeee....eee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....ee.hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeeeeeee............hhhhhhhhhhh..eeeeeeee...........eeeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..........eeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wd7 B -11 MRGSHHHHHHGSMVTMEEIRRAKRAEGLATILAISTATPPNCVIQADYPDYYFGITNSEHMTELKEKFKLLCEKSMIRKRHMCLTEEILKANPNMCLYMGTSLDARQDISLVEVPKLGKEAATKAIKEWGQPKSNITHLIFCTSAGVDMPGADYQLTRLIGLNPDVKRMMIYQQGCYAGATILRLAKDLAENNKGSRVLVVCSENTIPTFRGPSYTHIDSLVGQALFADGAAALIVGADPDTSIERPLYHIVSASQTLLPDSDGAIEGHIREAGLTVHLKKDVPEFFSANIEKSLVDAFTPIGISDWNSIFWIAHPGGPAILDQVEAKLGLKKDKLRASRHVMSEYGNMSSACVLFILDEMRNKCLEEGKATTGEGLDWGVLFGFGPGLTVETVVLHSLPI 389
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WD7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WD7)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (U3KRF0_9ROSI | U3KRF0)
molecular function
    GO:0050635    acridone synthase activity    Catalysis of the reaction: N-methylanthranilyl-CoA + 3 H(+) + 3 malonyl-CoA = 1,3-dihydroxy-N-methylacridone + 3 CO(2) + 4 CoA + H(2)O.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  3wd7
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3wd8