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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF YEAST ACETOHYDROXYACID SYNTHASE: A TARGET FOR HERBICIDAL INHIBITORS
 
Authors :  S. S. Pang, R. G. Duggleby, L. W. Guddat
Date :  17 Aug 01  (Deposition) - 16 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acetohydroxyacid Synthase, Acetolactate Synthase, Fad, Thiamin Diphosphate, Herbicide Inhibition, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Pang, R. G. Duggleby, L. W. Guddat
Crystal Structure Of Yeast Acetohydroxyacid Synthase: A Target For Herbicidal Inhibitors.
J. Mol. Biol. V. 317 249 2002
PubMed-ID: 11902841  |  Reference-DOI: 10.1006/JMBI.2001.5419
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACETOHYDROXY-ACID SYNTHASE
    Chains: A, B
    EC Number: 4.1.3.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MATURE CATALYTIC SUBUNIT
    Gene: ILV2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ACETOLACTATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
12HP3Ligand/IonDIHYDROGENPHOSPHATE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3K2Ligand/IonPOTASSIUM ION
4MG2Ligand/IonMAGNESIUM ION
5TPP2Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:343 , ASP A:350 , GLN A:506 , TRP A:508 , HOH A:772 , HOH A:1029 , HOH A:1033BINDING SITE FOR RESIDUE K A 696
02AC2SOFTWAREASP A:550 , ASN A:577 , TPP A:700 , HOH A:795 , HOH A:796BINDING SITE FOR RESIDUE MG A 699
03AC3SOFTWAREGLN B:343 , GLN B:506 , TRP B:508 , HOH B:802 , HOH B:1028 , HOH B:1034BINDING SITE FOR RESIDUE K B 1696
04AC4SOFTWAREASP B:550 , ASN B:577 , HOH B:748 , HOH B:794 , TPP B:1700BINDING SITE FOR RESIDUE MG B 1699
05AC5SOFTWAREGLY A:115 , GLY A:116 , GLN A:202 , HOH A:823 , TPP B:1700BINDING SITE FOR RESIDUE 2HP A 698
06AC6SOFTWAREHIS A:126 , HIS B:597 , THR B:598 , HIS B:599BINDING SITE FOR RESIDUE 2HP B 1697
07AC7SOFTWARETPP A:700 , GLY B:116 , GLN B:202 , HOH B:791BINDING SITE FOR RESIDUE 2HP B 1698
08AC8SOFTWAREVAL A:497 , GLY A:498 , GLN A:499 , HIS A:500 , GLY A:523 , MET A:525 , GLY A:549 , ASP A:550 , ALA A:551 , SER A:552 , MET A:555 , ASN A:577 , MG A:699 , HOH A:795 , HOH A:796 , HOH A:825 , HOH A:1011 , TYR B:113 , PRO B:114 , GLU B:139 , PRO B:165 , ASN B:169 , GLN B:202 , 2HP B:1698BINDING SITE FOR RESIDUE TPP A 700
09AC9SOFTWAREARG A:241 , GLY A:307 , ALA A:308 , GLY A:309 , ASN A:312 , THR A:334 , LEU A:335 , GLN A:336 , LEU A:352 , GLY A:353 , MET A:354 , HIS A:355 , GLY A:356 , GLY A:374 , ALA A:375 , ARG A:376 , ASP A:378 , ARG A:380 , VAL A:381 , GLU A:407 , VAL A:408 , ASN A:412 , GLY A:425 , ASP A:426 , ALA A:427 , HOH A:797 , HOH A:798 , HOH A:908 , HOH A:963 , HOH A:1000 , HOH A:1003 , PHE B:201BINDING SITE FOR RESIDUE FAD A 701
10BC1SOFTWARETYR A:113 , PRO A:114 , GLU A:139 , PRO A:165 , ASN A:169 , GLN A:202 , 2HP A:698 , VAL B:497 , GLY B:498 , GLN B:499 , HIS B:500 , GLY B:523 , MET B:525 , ASP B:550 , ALA B:551 , SER B:552 , MET B:555 , ASN B:577 , HOH B:748 , HOH B:794 , HOH B:831 , HOH B:1027 , MG B:1699BINDING SITE FOR RESIDUE TPP B 1700
11BC2SOFTWAREPHE A:201 , ARG B:241 , GLY B:307 , ALA B:308 , GLY B:309 , ASN B:312 , THR B:334 , LEU B:335 , MET B:351 , LEU B:352 , GLY B:353 , MET B:354 , HIS B:355 , GLY B:356 , GLY B:374 , ALA B:375 , ARG B:376 , ASP B:378 , ARG B:380 , VAL B:381 , PHE B:406 , GLU B:407 , VAL B:408 , ASN B:412 , GLY B:425 , ASP B:426 , ALA B:427 , MET B:502 , GLY B:520 , GLY B:521 , HOH B:741 , HOH B:777 , HOH B:828 , HOH B:863BINDING SITE FOR RESIDUE FAD B 1701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JSC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JSC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JSC)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.ILVB_YEAST533-552
 		  2A:533-552
B:533-552

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR108W1YMR108W.1XIII:484083-4861462064ILVB_YEAST1-6876872A:83-648 (gaps)
B:82-649 (gaps)		566
568

(-) 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:541
 aligned with ILVB_YEAST | P07342 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:566
                                    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       522       532       542       552       562       572       582       592       602       612       622       632       642      
           ILVB_YEAST    83 PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTGQVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATSGRPGPVLVDLPKDVTAAILRNPIPTKTTLPSNALNQLTSRAQDEFVMQSINKAADLINLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQEDPKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRAAAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSKIFPVKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRHVIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKPESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLFYEHRYSHTHQLNPDFIKLAEAMGLKGLRVKKQEELDAKLKEFVSTKGPVLLEVEVDKK 648
               SCOP domains d1jsca2 A:83-270 Acetohydroxyacid synthase catalytic subunit                                                                                                                                         d1jsca1 A:280-460 Acetohydroxyacid synthase catalytic subunit                                                                                                                        d1jsca3 A:461-648 Acetohydroxyacid synthase catalytic subunit                                                                                                                                SCOP domains
               CATH domains 1jscA01 A:83-280  [code=3.40.50.970, no name defined]                                                                                                                                                 1jscA02 A:281-458 TPP-binding domain                                                                                                                                              --------1jscA03 A:467-648  [code=3.40.50.970, no name defined]                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh........hhhhhh.....eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.....ee.hhhh..---------.hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhh...eee..............eeee.....hhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh.......ee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhhh...eeeeee...----------------........hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:83-648 (gaps) UniProt: 1-687 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 1jsc A  83 PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTGQVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATSGRPGPVLVDLPKDVTAAILRNPIPTKTTLPS---------AQDEFVMQSINKAADLINLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQEDPKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRAAAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSKIFPVKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRHVIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKPESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEE----------------SHTHQLNPDFIKLAEAMGLKGLRVKKQEELDAKLKEFVSTKGPVLLEVEVDKK 648
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       | -       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572      |  -         -   |   602       612       622       632       642      
                                                                                                                                                                                                                     270       280                                                                                                                                                                                                                                                                                                        579              596                                                    


Chain B from PDB  Type:PROTEIN  Length:550
 aligned with ILVB_YEAST | P07342 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:568
                                    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       511       521       531       541       551       561       571       581       591       601       611       621       631       641        
           ILVB_YEAST    82 EPDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTGQVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATSGRPGPVLVDLPKDVTAAILRNPIPTKTTLPSNALNQLTSRAQDEFVMQSINKAADLINLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQEDPKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRAAAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSKIFPVKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRHVIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKPESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLFYEHRYSHTHQLNPDFIKLAEAMGLKGLRVKKQEELDAKLKEFVSTKGPVLLEVEVDKKV 649
               SCOP domains d1jscb2 B:82-272 Acetohydroxyacid synthase catalytic subunit                                                                                                                                      d1jscb1 B:276-458 Acetohy droxyacid synthase catalytic subunit                                                                                                                              d1jscb3 B:464-649 Acetohydroxyacid synthase catalytic subunit                                                                                                                              SCOP domains
               CATH domains -1jscB01 B:83-280  [code=3.40.50.970, no name defined]                                                                                                                                                 1jscB02 B:281-458 TP P-binding domain                                                                                                                                                  ---1jscB03 B:467-648  [code=3.40.50.970, no name defined]                                                                                                                                - CATH domains
           Pfam domains (1) ----------TPP_enzyme_N-1jscB05 B:92-262                                                                                                                                              ----------   -------------TPP_enzyme_M -1jscB01 B:289-435                                                                                                                    ------  ---------------     --------------------------------TPP_enzyme_C-1jscB03 B:496-643                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) ----------TPP_enzyme_N-1jscB06 B:92-262                                                                                                                                              ----------   -------------TPP_enzyme_M -1jscB02 B:289-435                                                                                                                    ------  ---------------     --------------------------------TPP_enzyme_C-1jscB04 B:496-643                                                                                                                      ------ Pfam domains (2)
         Sec.struct. author ...ee......hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh........hhhhhh.....eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.....ee.hhh.....---..hhhhhhhhhhhhhhhhhhhhh..-.eeee.hhhhhh.hhhhhhhhhhhhh...eee.hhhh.........eeee.....hhhhhhhh.....eeee..........hhhhh........------.eee..hhhhh.......ee...hhhhhhhh........--.hhhhhhhhhhhhh.-----........hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh.......ee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhhh...eeeeee......eeeee...-..eeee......hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:82-649 (gaps) UniProt: 1-687 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                 1jsc B  82 EPDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTGQVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATSGRPGPVLVDLPKDVTAAILRNPIPTKTTLPSNA---LTSRAQDEFVMQSINKAADLINLAK-PVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQEDPKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRAA------IIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSKIFPV--RSEWFAQINKWKKEY-----EETPGSKIKPQTVIKKLSKVANDTGRHVIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKPESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF-EHRYSHTHQLNPDFIKLAEAMGLKGLRVKKQEELDAKLKEFVSTKGPVLLEVEVDKKV 649
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271|   |  281       291        |-|      311       321       331       341       351       361       371       381       391    |    - |     411       421       431       441  |    451      |  -  |    471       481       491       501       511       521       531       541       551       561       571       581        |-|      601       611       621       631       641        
                                                                                                                                                                                                                        272 276                     300 |                                                                                           396    403                                   441  |           458   464                                                                                                                           590 |                                                         
                                                                                                                                                                                                                                                      302                                                                                                                                           444                                                                                                                                                 592
   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  (3, 6)

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

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: FAD_DHS (82)
(-)
Clan: THDP-binding (106)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ILVB_YEAST | P07342)
molecular function
    GO:0003984    acetolactate synthase activity    Catalysis of the reaction: 2 pyruvate = 2-acetolactate + CO2.
    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:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
    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.
biological process
    GO:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    GO:0009099    valine biosynthetic process    The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.
cellular component
    GO:0005948    acetolactate synthase complex    A dimeric (a large and a small chain) or tetrameric (two large and two small chains) enzyme complex. Catalyzes the formation of acetolactate from pyruvate.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  1jsc
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  ILVB_YEAST | P07342
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ILVB_YEAST | P07342: 1n0h 1t9a 1t9b 1t9c 1t9d 5fem 5ims 5inu 5inv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JSC)