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(-) Description

Title :  CRYSTAL STRUCTURE OF A 3-KETOACYL-ACP REDUCTASE FROM SINORHIZOBIUM MELILOTI 1021
 
Authors :  D. Kumaran, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  22 Dec 11  (Deposition) - 11 Jan 12  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Psi-Biology, Structural Genomics, Protein Structure Initiative, Nysgrc, New York Structural Genomics Research Consortium, Rossmann Fold, Nad(P) Binding Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, S. C. Almo, S. Swaminathan
Crystal Structure Of A 3-Ketoacyl-Acp Reductase From Sinorhizobium Meliloti 1021
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DEHYDROGENASE, POSSIBLY 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.1.1.100
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RB1300, SM_B21474
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3V8B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V8B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V8B)

(-) Exons   (0, 0)

(no "Exon" information available for 3V8B)

(-) 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:257
 aligned with Q92U42_RHIME | Q92U42 from UniProtKB/TrEMBL  Length:260

    Alignment length:257
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       
         Q92U42_RHIME     4 PSPVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQMRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
               SCOP domains d3v8ba_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.............hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..............hhhhhh.........hhhhh....hhhhhhhhhhhhhhhhhh.....eeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8b A   4 PSPVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQmRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
                                    13        23        33        43        53        63     |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       
                                                                                            69-MSE                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q92U42_RHIME | Q92U42 from UniProtKB/TrEMBL  Length:260

    Alignment length:257
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       
         Q92U42_RHIME     4 PSPVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQMRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
               SCOP domains d3v8bb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..............hhhhhh.........hhhhh....hhhhhhhhhhhhhhhhhh.....eeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8b B   4 PSPVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQmRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
                                    13        23        33        43        53        63     |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       
                                                                                            69-MSE                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:255
 aligned with Q92U42_RHIME | Q92U42 from UniProtKB/TrEMBL  Length:260

    Alignment length:255
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
         Q92U42_RHIME     6 PVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQMRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
               SCOP domains d3v8bc_ C: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..............hhhhhh.........hhhhh....hhhhhhhhhhhhhhhhhh.....eeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8b C   6 PVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQmRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
                                    15        25        35        45        55        65   |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
                                                                                          69-MSE                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:256
 aligned with Q92U42_RHIME | Q92U42 from UniProtKB/TrEMBL  Length:260

    Alignment length:256
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
         Q92U42_RHIME     5 SPVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQMRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
               SCOP domains d3v8bd_ D: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..............hhhhhh.........hhhhh....hhhhhhhhhhhhhhhhhh.....eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v8b D   5 SPVALITGAGSGIGRATALALAADGVTVGALGRTRTEVEEVADEIVGAGGQAIALEADVSDELQmRNAVRDLVLKFGHLDIVVANAGINGVWAPIDDLKPFEWDETIAVNLRGTFLTLHLTVPYLKQRGGGAIVVVSSINGTRTFTTPGATAYTATKAAQVAIVQQLALELGKHHIRVNAVCPGAIETNISDNTKLRHEEETAIPVEWPKGQVPITDGQPGRSEDVAELIRFLVSERARHVTGSPVWIDGGQGLLR 260
                                    14        24        34        44        54        64    |   74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
                                                                                           69-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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V8B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V8B)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q92U42_RHIME | Q92U42)
molecular function
    GO:0004316    3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity    Catalysis of the reaction: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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