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(-) Description

Title :  THE CRYSTAL STRUCTURE OF KLEBSIELLA PNEUMONIAE ACETOLACTATE SYNTHASE WITH ENZYME-BOUND COFACTOR AND WITH AN UNUSUAL INTERMEDIATE
 
Authors :  S. S. Pang, R. G. Duggleby, R. L. Schowen, L. W. Guddat
Date :  09 Apr 03  (Deposition) - 04 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Acetolactate Synthase, Acetohydroxyacid Synthase, Thiamin Diphosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Pang, R. G. Duggleby, R. L. Schowen, L. W. Guddat
The Crystal Structures Of Klebsiella Pneumoniae Acetolactat Synthase With Enzyme-Bound Cofactor And With An Unusual Intermediate.
J. Biol. Chem. V. 279 2242 2004
PubMed-ID: 14557277  |  Reference-DOI: 10.1074/JBC.M304038200

(-) Compounds

Molecule 1 - ACETOLACTATE SYNTHASE, CATABOLIC
    ChainsA, B
    EC Number4.1.3.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET30A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneBUDB OR ILVK
    Organism ScientificKLEBSIELLA PNEUMONIAE
    Organism Taxid573
    SynonymALS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1HE32Ligand/Ion2-HYDROXYETHYL DIHYDROTHIACHROME DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1HE34Ligand/Ion2-HYDROXYETHYL DIHYDROTHIACHROME DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PEG16Ligand/IonDI(HYDROXYETHYL)ETHER
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:256 , GLY A:258 , ARG A:259 , GLN A:266 , ARG A:352 , ALA A:402 , ARG A:403 , LEU A:405 , TYR A:406 , HOH A:756BINDING SITE FOR RESIDUE PO4 A 697
02AC2SOFTWAREASP A:447 , ASP A:474 , GLY A:476 , HE3 A:700 , HOH A:740BINDING SITE FOR RESIDUE MG A 699
03AC3SOFTWAREARG B:259 , GLN B:266 , ARG B:352 , ALA B:402 , ARG B:403 , LEU B:405 , TYR B:406 , HOH B:752BINDING SITE FOR RESIDUE PO4 B 703
04AC4SOFTWAREASP B:447 , ASP B:474 , GLY B:476 , HE3 B:705 , HOH B:706BINDING SITE FOR RESIDUE MG B 704
05AC5SOFTWAREILE A:32 , PRO A:33 , GLU A:57 , PRO A:83 , ASN A:87 , MET A:394 , GLY A:395 , SER A:396 , PHE A:397 , GLN A:420 , MET A:422 , ASP A:447 , GLY A:448 , GLY A:449 , ASP A:474 , GLY A:476 , TYR A:477 , ASN A:478 , MET A:479 , VAL A:480 , TYR A:543 , MG A:699 , HOH A:740 , HOH A:763 , HOH A:776 , HOH A:959BINDING SITE FOR RESIDUE HE3 A 700
06AC6SOFTWAREILE B:32 , PRO B:33 , GLU B:57 , THR B:80 , PRO B:83 , ASN B:87 , MET B:394 , GLY B:395 , SER B:396 , PHE B:397 , GLN B:420 , MET B:422 , GLY B:446 , ASP B:447 , GLY B:448 , GLY B:449 , GLN B:452 , ASP B:474 , GLY B:476 , TYR B:477 , ASN B:478 , MET B:479 , TYR B:543 , MG B:704 , HOH B:706 , HOH B:759 , HOH B:769 , HOH B:934BINDING SITE FOR RESIDUE HE3 B 705
07AC7SOFTWARESER A:254 , GLN A:353 , ARG A:356 , PEG A:692 , HOH A:896 , ARG B:375BINDING SITE FOR RESIDUE PEG A 691
08AC8SOFTWAREARG A:356 , GLU A:357 , ARG A:362 , PEG A:691 , HOH A:997 , ARG B:378BINDING SITE FOR RESIDUE PEG A 692
09AC9SOFTWAREPRO A:498 , GLU A:506 , GLY A:509BINDING SITE FOR RESIDUE PEG A 693
10BC1SOFTWAREARG A:228 , HOH A:897 , HOH A:963 , ALA B:520 , THR B:524BINDING SITE FOR RESIDUE PEG A 694
11BC2SOFTWAREARG A:228 , ALA A:247 , HOH A:963BINDING SITE FOR RESIDUE PEG A 695
12BC3SOFTWAREPRO B:498 , GLY B:509BINDING SITE FOR RESIDUE PEG B 701
13BC4SOFTWARELEU B:262 , ASN B:417 , GLN B:420 , MET B:479 , HOH B:761BINDING SITE FOR RESIDUE PEG B 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:369 -Ala A:370
2Phe B:369 -Ala B:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.ILVB_KLEPN430-449
 
  2A:430-449
B:430-449
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.ILVB_KLEPN430-449
 
  4A:430-449
B:430-449

(-) Exons   (0, 0)

(no "Exon" information available for 1OZG)

(-) Sequences/Alignments

Asymmetric 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:549
 aligned with ILVB_KLEPN | P27696 from UniProtKB/Swiss-Prot  Length:559

    Alignment length:549
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545         
           ILVB_KLEPN     6 PVRQWAHGADLVVSQLEAQGVRQVFGIPGAKIDKVFDSLLDSSIRIIPVRHEANAAFMAAAVGRITGKAGVALVTSGPGCSNLITGMATANSEGDPVVALGGAVKRADKAKQVHQSMDTVAMFSPVTKYAIEVTAPDALAEVVSNAFRAAEQGRPGSAFVSLPQDVVDGPVSGKVLPASGAPQMGAAPDDAIDQVAKLIAQAKNPIFLLGLMASQPENSKALRRLLETSHIPVTSTYQAAGAVNQDNFSRFAGRVGLFNNQAGDRLLQLADLVICIGYSPVEYEPAMWNSGNATLVHIDVLPAYEERNYTPDVELVGDIAGTLNKLAQNIDHRLVLSPQAAEILRDRQHQRELLDRRGAQLNQFALHPLRIVRAMQDIVNSDVTLTVDMGSFHIWIARYLYTFRARQVMISNGQQTMGVALPWAIGAWLVNPERKVVSVSGDGGFLQSSMELETAVRLKANVLHLIWVDNGYNMVAIQEEKKYQRLSGVEFGPMDFKAYAESFGAKGFAVESAEALEPTLRAAMDVDGPAVVAIPVDYRDNPLLMGQLH 554
               SCOP domains d1ozga2 A:6-187 Catabolic acetolactate synthase                                                                                                                                       d1ozga1 A:188-366 Catabolic acetolactate synthase                                                                                                                                  d1ozga3 A:367-554 Catabolic acetolactate synthase                                                                                                                                            SCOP domains
               CATH domains 1ozgA01 A:6-188  [code=3.40.50.970, no name defined]                                                                                                                                   1ozgA02 A:189-363 TPP-binding domain                                                                                                                                           1ozgA03 A:364-554  [code=3.40.50.970, no name defined]                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhh....hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.eee..............hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh..eee.hhhh..........eeee......hhhhhhhhhh.eeeee..hhhhhhhhhh.....eeeeee.............eeee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhhh..eeeeeee...hhhhhhhhhhhhh..........hhhhhhhh...eeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ozg A   6 PVRQWAHGADLVVSQLEAQGVRQVFGIPGAKIDKVFDSLLDSSIRIIPVRHEANAAFMAAAVGRITGKAGVALVTSGPGCSNLITGMATANSEGDPVVALGGAVKRADKAKQVHQSMDTVAMFSPVTKYAIEVTAPDALAEVVSNAFRAAEQGRPGSAFVSLPQDVVDGPVSGKVLPASGAPQMGAAPDDAIDQVAKLIAQAKNPIFLLGLMASQPENSKALRRLLETSHIPVTSTYQAAGAVNQDNFSRFAGRVGLFNNQAGDRLLQLADLVICIGYSPVEYEPAMWNSGNATLVHIDVLPAYEERNYTPDVELVGDIAGTLNKLAQNIDHRLVLSPQAAEILRDRQHQRELLDRRGAQLNQFALHPLRIVRAMQDIVNSDVTLTVDMGSFHIWIARYLYTFRARQVMISNGQQTMGVALPWAIGAWLVNPERKVVSVSGDGGFLQSSMELETAVRLKANVLHLIWVDNGYNMVAIQEEKKYQRLSGVEFGPMDFKAYAESFGAKGFAVESAEALEPTLRAAMDVDGPAVVAIPVDYRDNPLLMGQLH 554
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545         

Chain B from PDB  Type:PROTEIN  Length:545
 aligned with ILVB_KLEPN | P27696 from UniProtKB/Swiss-Prot  Length:559

    Alignment length:550
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554
           ILVB_KLEPN     5 YPVRQWAHGADLVVSQLEAQGVRQVFGIPGAKIDKVFDSLLDSSIRIIPVRHEANAAFMAAAVGRITGKAGVALVTSGPGCSNLITGMATANSEGDPVVALGGAVKRADKAKQVHQSMDTVAMFSPVTKYAIEVTAPDALAEVVSNAFRAAEQGRPGSAFVSLPQDVVDGPVSGKVLPASGAPQMGAAPDDAIDQVAKLIAQAKNPIFLLGLMASQPENSKALRRLLETSHIPVTSTYQAAGAVNQDNFSRFAGRVGLFNNQAGDRLLQLADLVICIGYSPVEYEPAMWNSGNATLVHIDVLPAYEERNYTPDVELVGDIAGTLNKLAQNIDHRLVLSPQAAEILRDRQHQRELLDRRGAQLNQFALHPLRIVRAMQDIVNSDVTLTVDMGSFHIWIARYLYTFRARQVMISNGQQTMGVALPWAIGAWLVNPERKVVSVSGDGGFLQSSMELETAVRLKANVLHLIWVDNGYNMVAIQEEKKYQRLSGVEFGPMDFKAYAESFGAKGFAVESAEALEPTLRAAMDVDGPAVVAIPVDYRDNPLLMGQLH 554
               SCOP domains d1ozgb2 B:5-187 Catabolic acetolactate synthase                                                                                                                                        d1ozgb1 B:188-366 Catabolic acetolactate synthase                                                                                                                                  d1ozgb3 B:367-554 Catabolic acetolactate synthase                                                                                                                                            SCOP domains
               CATH domains 1ozgB01 B:5-188  [code=3.40.50.970, no name defined]                                                                                                                                    1ozgB02 B:189-362 TPP-binding domain                                                                                                                                           1ozgB03 B:364-554  [code=3.40.50.970, no name defined]                                                                                                                                          CATH domains
           Pfam domains (1) ------TPP_enzyme_N-1ozgB05 B:11-180                                                                                                                                             ---- -----------TPP_enzyme_M-1ozgB01 B:197-331                                                                                                         ------------------------------- -----------------------------TPP_enzyme_C-1ozgB03 B:393-539                                                                                                                     --------------- Pfam domains (1)
           Pfam domains (2) ------TPP_enzyme_N-1ozgB06 B:11-180                                                                                                                                             ---- -----------TPP_enzyme_M-1ozgB02 B:197-331                                                                                                         ------------------------------- -----------------------------TPP_enzyme_C-1ozgB04 B:393-539                                                                                                                     --------------- Pfam domains (2)
         Sec.struct. author ...eee.hhhhhhhhhhhhh...eeeee....hhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...---..hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.eee......-.......hhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhh..eee.hhhh..........eeee......hhhhhhhhhh.eeeee..hhhhhhhhhhh....eeeeee.............eeee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh-........hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhhh..eeeeeee...hhhhhhhhhhhhh..........hhhhhhhhh..eeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ozg B   5 YPVRQWAHGADLVVSQLEAQGVRQVFGIPGAKIDKVFDSLLDSSIRIIPVRHEANAAFMAAAVGRITGKAGVALVTSGPGCSNLITGMATANSEGDPVVALGGAVKRADKAKQ---SMDTVAMFSPVTKYAIEVTAPDALAEVVSNAFRAAEQGRPGSAFVSLPQDVVDGPVSGKVLPAS-APQMGAAPDDAIDQVAKLIAQAKNPIFLLGLMASQPENSKALRRLLETSHIPVTSTYQAAGAVNQDNFSRFAGRVGLFNNQAGDRLLQLADLVICIGYSPVEYEPAMWNSGNATLVHIDVLPAYEERNYTPDVELVGDIAGTLNKLAQNIDHRLVLSPQAAEILRDRQHQRELLDRR-AQLNQFALHPLRIVRAMQDIVNSDVTLTVDMGSFHIWIARYLYTFRARQVMISNGQQTMGVALPWAIGAWLVNPERKVVSVSGDGGFLQSSMELETAVRLKANVLHLIWVDNGYNMVAIQEEKKYQRLSGVEFGPMDFKAYAESFGAKGFAVESAEALEPTLRAAMDVDGPAVVAIPVDYRDNPLLMGQLH 554
                                    14        24        34        44        54        64        74        84        94       104       114  |   |124       134       144       154       164       174       184 |     194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554
                                                                                                                                          117 121                                                            184 |                                                                                                                                                                             362 |                                                                                                                                                                                              
                                                                                                                                                                                                               186                                                                                                                                                                               364                                                                                                                                                                                              

   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 Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: FAD_DHS (82)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ILVB_KLEPN | P27696)
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: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:0034077    butanediol metabolic process    The chemical reactions and pathways involving butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ILVB_KLEPN | P276961ozf 1ozh 5d6r 5dx6

(-) Related Entries Specified in the PDB File

1ozf THE SAME ENZYME WITHOUT A TRAPPED REACTION INTERMEDIATE