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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (TETRAGONAL FORM)
 
Authors :  M. Bellinzoni, P. M. Alzari
Date :  31 Jan 11  (Deposition) - 01 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase, Aldolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bellinzoni, K. Bastard, A. Perret, A. Zaparucha, N. Perchat, C. Vergne, T. Wagner, R. C. De Melo-Minardi, F. Artiguenave, G. N. Cohen, J. Weissenbach, M. Salanoubat, P. M. Alzari
3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold For An Uncommon Claisen-Type Condensation.
J. Biol. Chem. V. 286 27399 2011
PubMed-ID: 21632536  |  Reference-DOI: 10.1074/JBC.M111.253260

(-) Compounds

Molecule 1 - 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCRT7/CT-TOPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-276
    Organism Scientific: CANDIDATUS CLOACAMONAS ACIDAMINOVORANS
    Organism Taxid: 456827

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2MG1Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:46 , HIS A:48 , GLU A:230 , FMT A:1275 , HOH A:2296 , HOH A:2297BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:46 , HIS A:48 , SER A:82 , GLY A:84 , THR A:106 , ASN A:108 , GLU A:143 , ZN A:301 , HOH A:2296 , HOH A:2297BINDING SITE FOR RESIDUE FMT A1275
3AC3SOFTWAREHOH A:2007 , HOH A:2008 , HOH A:2009 , HOH A:2025 , HOH A:2115 , HOH A:2268BINDING SITE FOR RESIDUE MG A1276
4AC4SOFTWAREHIS B:46 , HIS B:48 , GLU B:230 , FMT B:1276 , HOH B:2287 , HOH B:2288BINDING SITE FOR RESIDUE ZN B 301
5AC5SOFTWAREHIS B:46 , HIS B:48 , SER B:82 , GLY B:84 , THR B:106 , ASN B:108 , GLU B:143 , ZN B:301 , HOH B:2287 , HOH B:2288BINDING SITE FOR RESIDUE FMT B1276

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y7E)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:165 -Pro A:166
2Asn B:165 -Pro B:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7E)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7E)

(-) 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:274
 aligned with KCE_CLOAI | B0VHH0 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:274
                                    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    
            KCE_CLOAI     1 MEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILAL 274
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee................hhhhhhhhhhhhhhhheeeeee.ee.....ee.hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhh..eeeee...eee..eee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh........eeeeee........hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7e A   1 HEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILAL 274
                                    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    


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with KCE_CLOAI | B0VHH0 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:278
                               1                                                                                                                                                                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267        
            KCE_CLOAI     - ---MEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eeee................hhhhhhhhhhhhhhhheeeeee.ee.....ee.hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhh..eeeee...eee..eee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhh........eeeeee........hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7e B  -2 HHHHEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 2Y7E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y7E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y7E)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KCE_CLOAI | B0VHH0)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019475    L-lysine catabolic process to acetate    The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetate.

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  2y7e
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 Related Entries

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

UniProtKB/Swiss-Prot
        KCE_CLOAI | B0VHH0: 2y7d 2y7f 2y7g

(-) Related Entries Specified in the PDB File

2y7d CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (ORTHOROMBIC FORM)
2y7f CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM C. CLOACAMONAS ACIDAMINOVORANS IN COMPLEX WITH THE SUBSTRATE 3-KETO-5-AMINOHEXANOATE
2y7g CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM C. CLOACAMONAS ACIDAMINOVORANS IN COMPLEX WITH THE PRODUCT ACETOACETATE