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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS PUTIDA 2-OXOISOVALERATE DEHYDROGENASE (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE, E1B)
 
Authors :  A. Aevarsson, K. Seger, S. Turley, J. R. Sokatch, W. G. J. Hol
Date :  24 Jun 99  (Deposition) - 18 Aug 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Heterotetramer, Thdp Cofactor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Aevarsson, K. Seger, S. Turley, J. R. Sokatch, W. G. Hol
Crystal Structure Of 2-Oxoisovalerate And Dehydrogenase And The Architecture Of 2-Oxo Acid Dehydrogenase Multienzyme Complexes.
Nat. Struct. Biol. V. 6 785 1999
PubMed-ID: 10426958  |  Reference-DOI: 10.1038/11563

(-) Compounds

Molecule 1 - 2-OXOISOVALERATE DEHYDROGENASE ALPHA-SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: PSEUDOMONAS PUTIDA
    Expression System Plasmid: PJRS174 (PKT230 DERIVATIVE)
    Expression System Taxid: 303
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
 
Molecule 2 - 2-OXOISOVALERATE DEHYDROGENASE BETA-SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: PSEUDOMONAS PUTIDA
    Expression System Plasmid: PJRS174 (PKT230 DERIVATIVE)
    Expression System Taxid: 303
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303

 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, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
1COI1Ligand/Ion2-OXO-4-METHYLPENTANOIC ACID
2MG1Ligand/IonMAGNESIUM ION
3MSE22Mod. Amino AcidSELENOMETHIONINE
4TDP1Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 1 (3, 48)
No.NameCountTypeFull Name
1COI2Ligand/Ion2-OXO-4-METHYLPENTANOIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3MSE44Mod. Amino AcidSELENOMETHIONINE
4TDP2Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:213 , ASN A:242 , TRP A:244 , TDP A:500 , HOH A:515BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREMSE A:107 , TDP A:500 , HOH A:619 , TYR B:88 , HIS B:131BINDING SITE FOR RESIDUE COI B 502
3AC3SOFTWARETYR A:133 , ARG A:134 , GLY A:182 , LEU A:184 , GLY A:212 , ASP A:213 , GLY A:214 , ALA A:215 , GLU A:218 , ASN A:242 , TRP A:244 , ALA A:245 , ILE A:246 , HIS A:312 , MG A:501 , HOH A:505 , HOH A:509 , HOH A:572 , HOH A:617 , GLN B:31 , ILE B:60 , GLU B:62 , GLN B:84 , TYR B:88 , COI B:502BINDING SITE FOR RESIDUE TDP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QS0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp B:255 -Pro B:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QS0)

(-) Exons   (0, 0)

(no "Exon" information available for 1QS0)

(-) 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:407
 aligned with ODBA_PSEPU | P09060 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:407
                                    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       
           ODBA_PSEPU     2 NEYAPLRLHVPEPTGRPGCQTDFSYLRLNDAGQARKPPVDVDAADTADLSYSLVRVLDEQGDAQGPWAEDIDPQILRQGMRAMLKTRIFDSRMVVAQRQKKMSFYMQSLGEEAIGSGQALALNRTDMCFPTYRQQSILMARDVSLVEMICQLLSNERDPLKGRQLPIMYSVREAGFFTISGNLATQFVQAVGWAMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVVNNQWAISTFQAIAGGESTTFAGRGVGCGIASLRVDGNDFVAVYAASRWAAERARRGLGPSLIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIGHWSEEEHQATTAEFEAAVIAAQKEAEQYGTLANGHIPSAASMFEDVYKEMPDHLRRQRQEL 408
               SCOP domains d1qs0a_ A: 2-oxoisovalerate dehydrogenase (E1B), PP module                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1qs0A00 A:2-408  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --OxoDH_E1alpha_N-1qs0A02 A:4-46             ----------------------------------E1_dh-1qs0A01 A:81-381                                                                                                                                                                                                                                                                                       --------------------------- Pfam domains
         Sec.struct. author .....................hhhhh...............hhhhhhhhhh.............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh....eee....hhhhhhhh..hhhhhhhhhhh.................hhhh........hhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee..ee..ee.hhhh......hhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhh....eeeeee...........hhhhh...hhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qs0 A   2 NEYAPLRLHVPEPTGRPGCQTDFSYLRLNDAGQARKPPVDVDAADTADLSYSLVRVLDEQGDAQGPWAEDIDPQILRQGmRAmLKTRIFDSRmVVAQRQKKmSFYmQSLGEEAIGSGQALALNRTDmCFPTYRQQSILmARDVSLVEmICQLLSNERDPLKGRQLPImYSVREAGFFTISGNLATQFVQAVGWAmASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVVNNQWAISTFQAIAGGESTTFAGRGVGCGIASLRVDGNDFVAVYAASRWAAERARRGLGPSLIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIGHWSEEEHQATTAEFEAAVIAAQKEAEQYGTLANGHIPSAASmFEDVYKEmPDHLRRQRQEL 408
                                    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       
                                                                                                          81-MSE       94-MSE  103-MSE                  128-MSE     140-MSE  149-MSE             169-MSE                    196-MSE                                                                                                                                                                                          389-MSE 397-MSE       
                                                                                                             84-MSE                107-MSE                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with ODBB_PSEPU | P09061 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:338
                                    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        
           ODBB_PSEPU     2 ATTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPISESGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSEMARLRYRSAGEFIAPLTLRMPCGGGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAEESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVMEV 339
               SCOP domains d1qs0b1 B:2-205 2-oxoisovalerate dehydrogenase (E1B), Pyr module                                                                                                                                            d1qs0b2 B:206-339 2-oxoisovalerate dehydrogenase E1b, C-domain                                                                         SCOP domains
               CATH domains 1qs0B01 B:2-205  [code=3.40.50.970, no name defined]                                                                                                                                                        1qs0B02 B:206-339  [code=3.40.50.920, no name defined]                                                                                 CATH domains
               Pfam domains --Transket_pyr-1qs0B01 B:4-182                                                                                                                                                       -----------------------------Transketolase_C-1qs0B02 B:212-329                                                                                     ---------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhhhh..eeeee..............hhhhhhh...eee...hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhh...hhhhhh........eeeeee.............hhhhhh.....eee...hhhhhhhhhhhhhhh...eeeeee.hhh.....................eee............eee.....eeee..hhhhhhhhhhhhhh...eeee..eee..hhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhh........eeee.........hhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qs0 B   2 ATTTmTmIQALRSAmDVmLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPISESGIVGTAVGmGAYGLRPVVEIQFADYFYPASDQIVSEmARLRYRSAGEFIAPLTLRmPCGGGIYGGQTHSQSPEAmFTQVCGLRTVmPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAEESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVmEV 339
                                | | 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     |  
                                6-MSE    16-MSE                                                  72-MSE                     100-MSE            119-MSE            138-MSE    149-MSE                                                                                                                                                                                     337-MSE
                                  8-MSE     19-MSE
   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, 3)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (4, 4)

Asymmetric Unit
(-)
Clan: THDP-binding (106)
(-)
Clan: no clan defined [family: OxoDH_E1alpha_N] (1)
(-)
Clan: no clan defined [family: Transketolase_C] (40)

(-) Gene Ontology  (6, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (ODBA_PSEPU | P09060)
molecular function
    GO:0003863    3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity    Catalysis of the reaction: 3-methyl-2-oxobutanoate + lipoamide = S-(2-methylpropanoyl)dihydrolipoamide + CO2.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016624    oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide.
biological process
    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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain B   (ODBB_PSEPU | P09061)
molecular function
    GO:0003863    3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity    Catalysis of the reaction: 3-methyl-2-oxobutanoate + lipoamide = S-(2-methylpropanoyl)dihydrolipoamide + 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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  1qs0
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 Related Entries

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

UniProtKB/Swiss-Prot
        ODBA_PSEPU | P09060: 2bp7
        ODBB_PSEPU | P09061: 2bp7

(-) Related Entries Specified in the PDB File

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