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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE FROM SINORHIZOBIUM MELILOTI
 
Authors :  R. Agarwal, 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 :  16 Aug 11  (Deposition) - 31 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. C. Almo, S. Swaminathan
Crystal Structure Of A Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Reductase From Sinorhizobium Meliloti
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RA1268, SMA2343
    Organism Common: ENSIFER MELILOTI
    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  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1HEZ2Ligand/IonHEXANE-1,6-DIOL
2SO411Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:220 , THR A:230 , ILE A:233 , HOH A:321 , HOH A:331 , GLN B:220 , THR B:230BINDING SITE FOR RESIDUE HEZ A 265
02AC2SOFTWAREARG A:219 , GLN A:220 , GLU A:223 , HOH A:724 , ARG B:219 , GLN B:220BINDING SITE FOR RESIDUE SO4 A 266
03AC3SOFTWAREASP A:4 , LYS A:30 , ARG A:81 , HOH A:314 , ARG D:131 , ASN D:173BINDING SITE FOR RESIDUE SO4 A 267
04AC4SOFTWAREPRO A:225 , GLN A:226 , HOH A:287 , HOH A:311 , LYS C:30 , HOH C:328BINDING SITE FOR RESIDUE SO4 A 268
05AC5SOFTWAREARG B:161 , HOH B:429 , HOH B:713 , ARG D:161BINDING SITE FOR RESIDUE SO4 B 265
06AC6SOFTWAREARG B:37 , GLN B:38 , ALA B:39 , HOH B:668BINDING SITE FOR RESIDUE SO4 B 266
07AC7SOFTWARESER B:13 , ALA B:35 , ARG B:36 , ARG B:37 , HOH B:370BINDING SITE FOR RESIDUE SO4 B 267
08AC8SOFTWAREGLN C:220 , THR C:230 , ILE C:233 , GLN D:220 , THR D:230BINDING SITE FOR RESIDUE HEZ C 265
09AC9SOFTWAREGLY C:11 , SER C:13 , ALA C:35 , ARG C:36 , HOH C:320 , HOH C:638BINDING SITE FOR RESIDUE SO4 C 266
10BC1SOFTWAREARG C:37 , GLN C:38 , ALA C:39 , HOH C:342 , HOH C:678BINDING SITE FOR RESIDUE SO4 C 267
11BC2SOFTWAREARG C:219 , GLN C:220 , HOH C:692 , ARG D:219 , GLN D:220 , HOH D:533BINDING SITE FOR RESIDUE SO4 C 268
12BC3SOFTWAREGLY D:11 , SER D:13 , ALA D:35 , ARG D:36 , HOH D:317 , HOH D:634 , HOH D:687BINDING SITE FOR RESIDUE SO4 D 265
13BC4SOFTWAREARG D:37 , GLN D:38 , ALA D:39BINDING SITE FOR RESIDUE SO4 D 266

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TFO)

(-) 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:216
 aligned with Q92XI4_RHIME | Q92XI4 from UniProtKB/TrEMBL  Length:240

    Alignment length:239
                              1                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228         
         Q92XI4_RHIME     - --MDKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVVESELAGTITHEETMAAMDTYRAIALQPADIARAVRQVIEAPQSVDTTEITIRPTA 237
               SCOP domains d3tfoa_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...-----------------------..hhhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfo A   1 MVMDKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVV-----------------------ALQPADIARAVRQVIEAPQSVDTTEITIRPTA 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   |     -         -       210       220       230         
                                                                                                                                                                                                                 184                     208                               


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q92XI4_RHIME | Q92XI4 from UniProtKB/TrEMBL  Length:240

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         Q92XI4_RHIME     1 MDKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVVESELAGTITHEETMAAMDTYRAIALQPADIARAVRQVIEAPQSVDTTEITIRPTA 237
               SCOP domains d3tfob_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...----------------------...hhhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfo B   3 MDKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVV----------------------IALQPADIARAVRQVIEAPQSVDTTEITIRPTA 239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 |       -         -    |  212       222       232       
                                                                                                                                                                                                               184                    207                                


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with Q92XI4_RHIME | Q92XI4 from UniProtKB/TrEMBL  Length:240

    Alignment length:239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
         Q92XI4_RHIME     2 DKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVVESELAGTITHEETMAAMDTYRAIALQPADIARAVRQVIEAPQSVDTTEITIRPTASGN 240
               SCOP domains d3tfoc_ C: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...-----------------------..hhhhhhhhhhhhhhh...eeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfo C   4 DKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVV-----------------------ALQPADIARAVRQVIEAPQSVDTTEITIRPTASGN 242
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183|        -         -    |  213       223       233         
                                                                                                                                                                                                              184                     208                                  


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with Q92XI4_RHIME | Q92XI4 from UniProtKB/TrEMBL  Length:240

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q92XI4_RHIME     1 MDKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVVESELAGTITHEETMAAMDTYRAIALQPADIARAVRQVIEAPQSVDTTEITIRPTAS 238
               SCOP domains d3tfod_ D: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....--------------------....hhhhhhhhhhhhhhh...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfo D   3 MDKVILITGASGGIGEGIARELGVAGAKILLGARRQARIEAIATEIRDAGGTALAQVLDVTDRHSVAAFAQAAVDTWGRIDVLVNNAGVMPLSPLAAVKVDEWERMIDVNIKGVLWGIGAVLPIMEAQRSGQIINIGSIGALSVVPTAAVYCATKFAVRAISDGLRQESTNIRVTCVNPGVVE--------------------AIALQPADIARAVRQVIEAPQSVDTTEITIRPTAS 240
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  |      -         -   |   212       222       232        
                                                                                                                                                                                                                185                  206
   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 3TFO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q92XI4_RHIME | Q92XI4)
molecular function
    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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  3tfo
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