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(-) Description

Title :  STRUCTURE OF L-2-KETO-3-DEOXYARABONATE DEHYDRATASE COMPLEX WITH PYRUVATE
 
Authors :  N. Shimada, B. Mikami
Date :  17 Dec 08  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dhdps/Nal Family, Complex, Pyruvate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shimada, B. Mikami, S. Watanabe, T. Kodaki, K. Makino
Structural Analysis Of L -2-Keto-3-Deoxyarabonate Dehydratase An Enzyme Involved In An Alternative Bacterial Pathway Of L-Arabinose Metabolism In Complex With Pyruvate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-2-KETO-3-DEOXYARABONATE DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AZOSPIRILLUM BRASILENSE
    Organism Taxid: 192

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1KPI2Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
2NA2Ligand/IonSODIUM ION
3PO47Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:220 , GLU A:303 , ALA A:306 , ARG A:310 , HOH A:694 , HOH A:820 , HOH A:858 , HOH A:944 , HOH A:1047BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREGLU A:184 , THR A:185 , GLY A:187 , ALA A:188 , GLU A:210 , THR A:214 , ARG A:267 , HOH A:510 , HOH A:513 , HOH A:695 , HOH A:816BINDING SITE FOR RESIDUE PO4 A 404
3AC3SOFTWAREARG A:288 , PRO A:289 , HIS A:291 , MET A:293 , GLU A:295 , HOH A:566 , HOH A:623 , HOH A:958 , HOH A:1114BINDING SITE FOR RESIDUE PO4 A 405
4AC4SOFTWAREKPI A:182 , GLU A:184 , HOH A:1087BINDING SITE FOR RESIDUE NA A 409
5AC5SOFTWAREHIS B:220 , ALA B:306 , ARG B:310 , HOH B:756 , HOH B:786 , HOH B:853 , HOH B:1001BINDING SITE FOR RESIDUE PO4 B 402
6AC6SOFTWAREGLU B:184 , THR B:185 , GLY B:187 , ALA B:188 , GLU B:210 , THR B:214 , ARG B:267 , HOH B:567 , HOH B:591 , HOH B:636 , HOH B:872BINDING SITE FOR RESIDUE PO4 B 403
7AC7SOFTWAREARG B:44 , ASP B:47 , HOH B:724 , HOH B:1091BINDING SITE FOR RESIDUE PO4 B 406
8AC8SOFTWAREASP A:312 , ARG A:317 , ASP B:234 , ARG B:317 , HOH B:646 , HOH B:1026BINDING SITE FOR RESIDUE PO4 B 407
9AC9SOFTWAREKPI B:182 , GLU B:184 , HOH B:895 , HOH B:1046BINDING SITE FOR RESIDUE NA B 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:291 -Pro A:292
2His B:291 -Pro B:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FKR)

(-) 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:304
 aligned with KDADA_AZOBR | Q1JUQ0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:304
                                    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    
          KDADA_AZOBR     6 TPRHRGIFPVVPTTFADTGELDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 309
               SCOP domains d3fkra_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..............hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh...ee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkr A  17 TPRHRGIFPVVPTTFADTGDLDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFkIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 320
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     | 186       196       206       216       226       236       246       256       266       276       286       296       306       316    
                                                                                                                                                                                               182-KPI                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:304
 aligned with KDADA_AZOBR | Q1JUQ0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:304
                                    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    
          KDADA_AZOBR     6 TPRHRGIFPVVPTTFADTGELDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 309
               SCOP domains d3fkrb_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..............hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh...ee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkr B  17 TPRHRGIFPVVPTTFADTGDLDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFkIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 320
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     | 186       196       206       216       226       236       246       256       266       276       286       296       306       316    
                                                                                                                                                                                               182-KPI
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KDADA_AZOBR | Q1JUQ0)
molecular function
    GO:0047449    2-dehydro-3-deoxy-L-arabinonate dehydratase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + 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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019570    L-arabinose catabolic process to 2-oxoglutarate    The chemical reactions and pathways resulting in the breakdown of L-arabinose into other compounds, including 2-oxoglutarate.
    GO:0019568    arabinose catabolic process    The chemical reactions and pathways resulting in the breakdown of arabinose, arabino-pentose.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        KDADA_AZOBR | Q1JUQ0: 3fkk

(-) Related Entries Specified in the PDB File

3fkk THE SAME NATIVE PROTEIN