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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE)
 
Authors :  M. Bellinzoni, P. M. Alzari
Date :  31 Jan 11  (Deposition) - 01 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
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, C, D
    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
    Fragment: RESIDUES 2-276
    Organism Scientific: CANDIDATUS CLOACAMONAS ACIDAMINOVORANS
    Organism Taxid: 456827

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1KMH4Ligand/Ion(5S)-5-AMINO-3-OXO-HEXANOIC ACID
2MG1Ligand/IonMAGNESIUM ION
3ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:46 , HIS A:48 , GLU A:230 , KMH A:1276 , HOH A:2236BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREGLU A:14 , HIS A:46 , HIS A:48 , SER A:82 , GLY A:84 , GLY A:85 , VAL A:87 , THR A:106 , ASN A:108 , PHE A:114 , TYR A:145 , GLU A:230 , ZN A:301 , HOH A:2007 , HOH A:2236 , HOH A:2237BINDING SITE FOR RESIDUE KMH A1276
3AC3SOFTWAREHIS B:46 , HIS B:48 , GLU B:230 , KMH B:1276 , HOH B:2228BINDING SITE FOR RESIDUE ZN B 301
4AC4SOFTWAREGLU B:14 , HIS B:46 , HIS B:48 , SER B:82 , GLY B:84 , GLY B:85 , VAL B:87 , THR B:106 , ASN B:108 , PHE B:114 , TYR B:145 , GLU B:230 , ZN B:301 , HOH B:2011 , HOH B:2228BINDING SITE FOR RESIDUE KMH B1276
5AC5SOFTWAREHIS C:46 , HIS C:48 , GLU C:230 , KMH C:1276 , HOH C:2198BINDING SITE FOR RESIDUE ZN C 301
6AC6SOFTWAREGLU C:14 , HIS C:46 , HIS C:48 , SER C:82 , GLY C:84 , GLY C:85 , VAL C:87 , THR C:106 , ASN C:108 , PHE C:119 , TYR C:145 , GLU C:230 , ZN C:301 , HOH C:2198BINDING SITE FOR RESIDUE KMH C1276
7AC7SOFTWAREHIS D:46 , HIS D:48 , GLU D:230 , KMH D:1276 , HOH D:2209BINDING SITE FOR RESIDUE ZN D 301
8AC8SOFTWAREGLU D:14 , HIS D:46 , HIS D:48 , SER D:82 , GLY D:84 , GLY D:85 , VAL D:87 , THR D:106 , ASN D:108 , PHE D:119 , TYR D:145 , GLU D:230 , ZN D:301 , HOH D:2008 , HOH D:2209BINDING SITE FOR RESIDUE KMH D1276
9AC9SOFTWAREHOH A:2013 , HOH B:2086 , HOH B:2087 , ASP D:61 , GLU D:65 , HOH D:2059BINDING SITE FOR RESIDUE MG D1277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y7F)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:165 -Pro A:166
2Asn B:165 -Pro B:166
3Asn C:165 -Pro C:166
4Asn D:165 -Pro D:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7F)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7F)

(-) 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:277
 aligned with KCE_CLOAI | B0VHH0 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:277
                              1                                                                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       
            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
                 2y7f A  -1 HHHEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       


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..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh........eeeeee........hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..eeee......eee..ee..hhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y7f 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      


Chain C from PDB  Type:PROTEIN  Length:277
 aligned with KCE_CLOAI | B0VHH0 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:277
                              1                                                                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       
            KCE_CLOAI     - --MEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee................hhhhhhhhhhhhhhhh..eeee.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
                 2y7f C  -1 HHHEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       


Chain D from PDB  Type:PROTEIN  Length:277
 aligned with KCE_CLOAI | B0VHH0 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:277
                              1                                                                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       
            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..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh........eeeeee........hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..eeee......eee..ee..hhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7f D  -1 HHHEPLILTAAITGAETTRADQPNLPITPEEQAKEAKACFEAGARVIHLHIREDDGRPSQRLDRFQEAISAIREVVPEIIIQISTGGAVGESFDKRLAPLALKPEMATLNAGTLNFGDDIFINHPADIIRLAEAFKQYNVVPEVEVYESGMVDAVARLIKKGIITQNPLHIQFVLGVPGGMSGKPKNLMYMMEHLKEEIPTATWAVAGIGRWHIPTSLIAMVTGGHIRCGFEDNIFYHKGVIAESNAQLVARLARIAKEIGRPLATPEQAREILALN 275
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
   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  (0, 0)

(no "SCOP Domain" information available for 2Y7F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y7F)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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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  2y7f
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 Related Entries

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

UniProtKB/Swiss-Prot
        KCE_CLOAI | B0VHH0: 2y7d 2y7e 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)
2y7e CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (TETRAGONAL FORM)
2y7g CRYSTAL STRUCTURE OF THE 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME (KCE) FROM C. CLOACAMONAS ACIDAMINOVORANS IN COMPLEX WITH THE PRODUCT ACETOACETATE