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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM C. CLOACAMONAS ACIDAMINOVORANS IN COMPLEX WITH THE PRODUCT ACETOACETATE
 
Authors :  M. Bellinzoni, P. M. Alzari
Date :  31 Jan 11  (Deposition) - 01 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
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  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1AAE2Ligand/IonACETOACETIC ACID
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1AAE4Ligand/IonACETOACETIC ACID
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:46 , HIS A:48 , GLU A:230 , AAE A:1276 , HOH A:2265BINDING 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 , TYR A:145 , VAL A:172 , ARG A:226 , GLU A:230 , ZN A:301 , HOH A:2265BINDING SITE FOR RESIDUE AAE A1276
3AC3SOFTWAREGLU A:242 , SER A:243 , HOH A:2244 , HOH A:2266 , HOH A:2267 , HOH A:2268 , LEU B:60BINDING SITE FOR RESIDUE GOL A1277
4AC4SOFTWAREHOH A:2011 , HOH A:2012 , HOH A:2013 , HOH A:2029 , HOH A:2107 , HOH A:2244BINDING SITE FOR RESIDUE MG A1278
5AC5SOFTWAREHOH A:2007 , HOH A:2017 , HOH A:2021 , HOH A:2112 , HOH A:2140BINDING SITE FOR RESIDUE MG A1279
6AC6SOFTWAREHIS B:46 , HIS B:48 , GLU B:230 , AAE B:1276 , HOH B:2230BINDING SITE FOR RESIDUE ZN B 301
7AC7SOFTWAREHIS B:46 , HIS B:48 , SER B:82 , GLY B:84 , THR B:106 , ASN B:108 , GLU B:143 , TYR B:145 , VAL B:172 , ARG B:226 , GLU B:230 , ZN B:301 , HOH B:2230BINDING SITE FOR RESIDUE AAE B1276

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y7G)

(-) 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 2Y7G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7G)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7G)

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

    Alignment length:276
                             1                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      
            KCE_CLOAI     - -MEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
               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..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhh........eeeeee........hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..eeee......eee..ee..hhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y7g A   0 HHEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      


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

    Alignment length:276
                             1                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      
            KCE_CLOAI     - -MEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
               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..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhh........eeeeee........hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh...eeee......eee..ee..hhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y7g B   0 HHEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2Y7G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y7G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y7G)

(-) 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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  2y7g
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 Related Entries

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

UniProtKB/Swiss-Prot
        KCE_CLOAI | B0VHH0: 2y7d 2y7e 2y7f

(-) 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)
2y7e CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (TETRAGONAL 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