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(-) Description

Title :  CLAVULANIC ACID DEHYDROGENASE: STRUCTURAL AND BIOCHEMICAL ANALYSIS OF THE FINAL STEP IN THE BIOSYNTHESIS OF THE BETA-LACTAMASE INHIBITOR CLAVULANIC ACID
 
Authors :  A. K. Mackenzie, N. J. Kershaw, H. Hernandez, C. V. Robinson, C. J. Schof I. Andersson
Date :  29 Nov 06  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Short-Chain Dehydrogenase/Reductase, Oxidoreductase, Antibiotic Biosynthesis, Beta-Lactamase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Mackenzie, N. J. Kershaw, H. Hernandez, C. V. Robinson, C. J. Schofield, I. Andersson
Clavulanic Acid Dehydrogenase: Structural And Biochemical Analysis Of The Final Step In The Biosynthesis Of The Beta-Lactamase Inhibitor Clavulanic Acid
Biochemistry V. 46 1523 2007
PubMed-ID: 17279617  |  Reference-DOI: 10.1021/BI061978X

(-) Compounds

Molecule 1 - CLAVALDEHYDE DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: STREPTOMYCES CLAVULIGERUS
    Organism Taxid: 1901
    Strain: NRRL3585
    Synonym: CLAVULANIC ACID DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1J014Ligand/Ion(2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLICACID
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , SER A:16 , SER A:17 , GLY A:18 , ILE A:19 , ALA A:38 , ARG A:39 , ARG A:40 , LEU A:63 , ASP A:64 , VAL A:65 , ASN A:91 , ALA A:92 , GLY A:93 , THR A:114 , MET A:140 , SER A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , THR A:187 , THR A:188 , THR A:190 , GLU A:191 , LEU A:192 , J01 A:1249 , HOH A:2015 , HOH A:2062 , HOH A:2063 , HOH A:2064 , HOH A:2065 , HOH A:2066 , HOH A:2067BINDING SITE FOR RESIDUE NDP A1248
2AC2SOFTWAREMET A:95 , SER A:142 , ILE A:143 , ALA A:144 , ALA A:152 , TYR A:155 , GLN A:156 , THR A:187 , TYR A:205 , ARG A:208 , NDP A:1248 , HOH A:2033 , HOH A:2058 , HOH A:2068BINDING SITE FOR RESIDUE J01 A1249
3AC3SOFTWAREGLN A:69 , GLY B:14 , SER B:16 , SER B:17 , GLY B:18 , ILE B:19 , ALA B:38 , ARG B:39 , ARG B:40 , LEU B:63 , ASP B:64 , VAL B:65 , ASN B:91 , ALA B:92 , GLY B:93 , THR B:114 , MET B:140 , SER B:141 , SER B:142 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , THR B:187 , THR B:188 , THR B:190 , GLU B:191 , LEU B:192 , J01 B:1249 , HOH B:2001 , HOH B:2003 , HOH B:2007 , HOH B:2054 , HOH B:2055BINDING SITE FOR RESIDUE NDP B1248
4AC4SOFTWAREMET B:95 , LEU B:97 , SER B:142 , ILE B:143 , ALA B:144 , ALA B:152 , TYR B:155 , GLN B:156 , THR B:187 , TYR B:205 , ARG B:208 , NDP B:1248 , HOH B:2051BINDING SITE FOR RESIDUE J01 B1249
5AC5SOFTWAREGLY C:14 , SER C:16 , SER C:17 , GLY C:18 , ILE C:19 , ALA C:38 , ARG C:39 , ARG C:40 , LEU C:63 , ASP C:64 , VAL C:65 , ASN C:91 , ALA C:92 , GLY C:93 , THR C:114 , MET C:140 , SER C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , THR C:187 , THR C:188 , THR C:190 , GLU C:191 , LEU C:192 , J01 C:1249 , HOH C:2003 , HOH C:2051 , HOH C:2070 , HOH C:2071 , HOH C:2072BINDING SITE FOR RESIDUE NDP C1248
6AC6SOFTWAREMET C:95 , SER C:142 , ALA C:144 , ALA C:152 , TYR C:155 , GLN C:156 , THR C:187 , TYR C:205 , ARG C:208 , NDP C:1248 , HOH C:2067 , HOH C:2073BINDING SITE FOR RESIDUE J01 C1249
7AC7SOFTWAREGLY D:14 , SER D:16 , SER D:17 , GLY D:18 , ILE D:19 , ALA D:38 , ARG D:39 , ARG D:40 , LEU D:63 , ASP D:64 , VAL D:65 , ASN D:91 , ALA D:92 , GLY D:93 , THR D:114 , MET D:140 , SER D:141 , SER D:142 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , THR D:187 , THR D:188 , THR D:190 , GLU D:191 , LEU D:192 , J01 D:1249 , HOH D:2054 , HOH D:2055BINDING SITE FOR RESIDUE NDP D1248
8AC8SOFTWAREMET D:95 , SER D:142 , ALA D:144 , ALA D:152 , TYR D:155 , GLN D:156 , THR D:187 , TYR D:205 , ARG D:208 , NDP D:1248 , HOH D:2052 , HOH D:2056BINDING SITE FOR RESIDUE J01 D1249

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JAP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JAP)

(-) 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:245
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         Q9LCV7_STRCL     3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2japa_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jap A   3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         Q9LCV7_STRCL     3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2japb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jap B   3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     


Chain C from PDB  Type:PROTEIN  Length:246
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
         Q9LCV7_STRCL     2 PSALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2japc_ C: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jap C   2 PSALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain D from PDB  Type:PROTEIN  Length:245
 aligned with Q9LCV7_STRCL | Q9LCV7 from UniProtKB/TrEMBL  Length:247

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         Q9LCV7_STRCL     3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
               SCOP domains d2japd_ D: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jap D   3 SALQGKVALITGASSGIGEATARALAAEGAAVAIAARRVEKLRALGDELTAAGAKVHVLELDVADRQGVDAAVASTVEALGGLDILVNNAGIMLLGPVEDADTTDWTRMIDTNLLGLMYMTRAALPHLLRSKGTVVQMSSIAGRVNVRNAAVYQATKFGVNAFSETLRQEVTERGVRVVVIEPGTTDTELRGHITHTATKEMYEQRISQIRKLQAQDIAEAVRYAVTAPHHATVHEIFIRPTDQV 247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9LCV7_STRCL | Q9LCV7)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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 Related Entries

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        Q9LCV7_STRCL | Q9LCV7: 2jah

(-) Related Entries Specified in the PDB File

2jah BIOCHEMICAL AND STRUCTURAL ANALYSIS OF THE CLAVULANIC ACID DEHYDEOGENASE (CAD) FROM STREPTOMYCES CLAVULIGERUS