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(-) Description

Title :  STRUCTURE OF THE 2-AMINO-3-KETOBUTYRATE COENZYME A LIGASE (KBL) FROM COXIELLA BURNETII
 
Authors :  J. Cheung, M. C. Franklin, M. Rudolph, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 21 Sep 11  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Energy Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - 2-AMINO-3-KETOBUTYRATE COENZYME A LIGASE
    Chains: A, B
    EC Number: 2.3.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CBU_0111, KBL
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 227377
    Strain: RSA493

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric/Biological Unit (2, 22)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:108 , CYS A:109 , PHE A:110 , HIS A:134 , SER A:136 , ASP A:208 , SER A:210 , HIS A:211 , THR A:239 , LYS A:242 , GLY A:249 , HOH A:422 , SER B:272 , ASN B:273BINDING SITE FOR RESIDUE PLP A 397
2AC2SOFTWAREPHE A:271 , SER A:272 , ASN A:273 , SER B:108 , CYS B:109 , PHE B:110 , HIS B:134 , ASP B:208 , SER B:210 , HIS B:211 , THR B:239 , LYS B:242 , HOH B:484BINDING SITE FOR RESIDUE PLP B 397

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Mse A:156 -Gly A:157
2Tyr A:356 -Pro A:357
3Mse B:156 -Gly B:157
4Tyr B:356 -Pro B:357

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TQX)

(-) 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:396
 aligned with Q83F40_COXBU | Q83F40 from UniProtKB/TrEMBL  Length:396

    Alignment length:396
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390      
         Q83F40_COXBU     1 MQEILSQLNKEIEGLKKAGLYKSERIITSPQNAEIKVGEKEVLNFCANNYLGLADHPALIKTAQTVVEQYGFGMASVRFICGTQTIHKELEKDISEFLGTDDTILYSSCFDANGGLFETLLGPEDAIISDELNHASIIDGIRLCKAQRYRYKNNAMGDLEAKLKEADEKGARFKLIATDGVFSMDGIIADLKSICDLADKYNALVMVDDSHAVGFIGENGRGTPEYCGVADRVDILTGTLGKALGGASGGYTSGHKEIIEWLRNRSRPYLFSNTVAPVIVATSLKVLELLKTEGPQLRKQLQENSRYFRAGMEKLGFQLVPGNHPIIPVMLGDAQLATNMADHLLQEGIYVVGFSYPVVPMGKARIRVQMSAVHTQQQLDRAIEAFGQVGKKLGAI 396
               SCOP domains d3tqxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh................eeee..eeeee...........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh..eeeee.............hhhhhh.......eeeee..........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeehhhhhhhhhhhhhhh.ee..ee.........eeeeee.....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tqx A   1 mQEILSQLNKEIEGLKKAGLYKSERIITSPQNAEIKVGEKEVLNFCANNYLGLADHPALIKTAQTVVEQYGFGmASVRFICGTQTIHKELEKDISEFLGTDDTILYSSCFDANGGLFETLLGPEDAIISDELNHASIIDGIRLCKAQRYRYKNNAmGDLEAKLKEADEKGARFKLIATDGVFSmDGIIADLKSICDLADKYNALVmVDDSHAVGFIGENGRGTPEYCGVADRVDILTGTLGKALGGASGGYTSGHKEIIEWLRNRSRPYLFSNTVAPVIVATSLKVLELLKTEGPQLRKQLQENSRYFRAGmEKLGFQLVPGNHPIIPVmLGDAQLATNmADHLLQEGIYVVGFSYPVVPmGKARIRVQmSAVHTQQQLDRAIEAFGQVGKKLGAI 396
                            |       10        20        30        40        50        60        70   |    80        90       100       110       120       130       140       150     | 160       170       180   |   190       200     | 210       220       230       240       250       260       270       280       290       300       310 |     320       330       340       350       360|      370       380       390      
                            |                                                                       74-MSE                                                                           156-MSE                     184-MSE               206-MSE                                                                                                   312-MSE           330-MSE   340-MSE              361-MSE  370-MSE                      
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with Q83F40_COXBU | Q83F40 from UniProtKB/TrEMBL  Length:396

    Alignment length:396
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390      
         Q83F40_COXBU     1 MQEILSQLNKEIEGLKKAGLYKSERIITSPQNAEIKVGEKEVLNFCANNYLGLADHPALIKTAQTVVEQYGFGMASVRFICGTQTIHKELEKDISEFLGTDDTILYSSCFDANGGLFETLLGPEDAIISDELNHASIIDGIRLCKAQRYRYKNNAMGDLEAKLKEADEKGARFKLIATDGVFSMDGIIADLKSICDLADKYNALVMVDDSHAVGFIGENGRGTPEYCGVADRVDILTGTLGKALGGASGGYTSGHKEIIEWLRNRSRPYLFSNTVAPVIVATSLKVLELLKTEGPQLRKQLQENSRYFRAGMEKLGFQLVPGNHPIIPVMLGDAQLATNMADHLLQEGIYVVGFSYPVVPMGKARIRVQMSAVHTQQQLDRAIEAFGQVGKKLGAI 396
               SCOP domains d3tqxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh................eeee..eeeee...........hhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhh....eeeee......hhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhh.eeeee.............hhhhhhh......eeeee..........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhhhee..ee.........eeeeee.....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tqx B   1 mQEILSQLNKEIEGLKKAGLYKSERIITSPQNAEIKVGEKEVLNFCANNYLGLADHPALIKTAQTVVEQYGFGmASVRFICGTQTIHKELEKDISEFLGTDDTILYSSCFDANGGLFETLLGPEDAIISDELNHASIIDGIRLCKAQRYRYKNNAmGDLEAKLKEADEKGARFKLIATDGVFSmDGIIADLKSICDLADKYNALVmVDDSHAVGFIGENGRGTPEYCGVADRVDILTGTLGKALGGASGGYTSGHKEIIEWLRNRSRPYLFSNTVAPVIVATSLKVLELLKTEGPQLRKQLQENSRYFRAGmEKLGFQLVPGNHPIIPVmLGDAQLATNmADHLLQEGIYVVGFSYPVVPmGKARIRVQmSAVHTQQQLDRAIEAFGQVGKKLGAI 396
                            |       10        20        30        40        50        60        70   |    80        90       100       110       120       130       140       150     | 160       170       180   |   190       200     | 210       220       230       240       250       260       270       280       290       300       310 |     320       330       340       350       360|      370       380       390      
                            1-MSE                                                                   74-MSE                                                                           156-MSE                     184-MSE               206-MSE                                                                                                   312-MSE           330-MSE   340-MSE              361-MSE  370-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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q83F40_COXBU | Q83F40)
molecular function
    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:0008890    glycine C-acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + glycine = L-2-amino-3-oxobutanoate + CoA + H(+).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    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).
biological process
    GO:0019518    L-threonine catabolic process to glycine    The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form to form 2-amino-3-oxobutanoate, which is subsequently converted to glycine.
    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.
    GO:0006567    threonine catabolic process    The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

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 Related Entries

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