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(-) Description

Title :  CRYSTAL STRUCTURE OF A BETA-KETOACYL REDUCTASE FABG4 FROM MYCOBACTERIUM TUBERCULOSIS H37RV COMPLEXED WITH NAD+ AND HEXANOYL-COA AT 2.5 ANGSTROM RESOLUTION
 
Authors :  D. Dutta, S. Bhattacharyya, A. K. Das
Date :  10 Dec 11  (Deposition) - 28 Nov 12  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Ketoreductase, High Molecular Weight Fabg(Hmwfabg), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Dutta, S. Bhattacharyya, A. Roychowdhury, R. Biswas, A. K. Das
Crystal Structure Of Hexanoyl-Coa Bound To Beta-Ketoacyl Reductase Fabg4 Of Mycobacterium Tuberculosis
Biochem. J. V. 450 127 2013
PubMed-ID: 23163771  |  Reference-DOI: 10.1042/BJ20121107

(-) Compounds

Molecule 1 - 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
    Chains: A
    EC Number: 1.1.1.100
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABG-1, FABG4, MT0256, RV0242C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: PROBABLE 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE FABG4 (3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1HXC1Ligand/IonHEXANOYL-COENZYME A
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZPG1Ligand/Ion(2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1HXC2Ligand/IonHEXANOYL-COENZYME A
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZPG2Ligand/Ion(2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:220 , ARG A:223 , GLY A:224 , ILE A:225 , ASP A:244 , VAL A:245 , LEU A:266 , ASP A:267 , VAL A:268 , ASN A:295 , ALA A:296 , ILE A:298 , VAL A:318 , LEU A:345 , SER A:346 , SER A:347 , TYR A:360 , LYS A:364 , PRO A:390 , GLY A:391 , ILE A:393 , GLN A:396 , HXC A:502 , HOH A:630 , HOH A:709BINDING SITE FOR RESIDUE NAD A 501
2AC2SOFTWAREGLU A:151 , ARG A:153 , GLY A:297 , THR A:299 , ASP A:301 , LYS A:302 , LEU A:303 , ASN A:306 , ASN A:354 , ARG A:355 , NAD A:501 , HOH A:669BINDING SITE FOR RESIDUE HXC A 502
3AC3SOFTWAREGLU A:338 , ALA A:379 , ALA A:380BINDING SITE FOR RESIDUE ZPG A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V1U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:71 -Gly A:72
2Thr A:395 -Gln A:396

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V1U)

(-) Exons   (0, 0)

(no "Exon" information available for 3V1U)

(-) 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:416
 aligned with O53665_MYCTO | O53665 from UniProtKB/TrEMBL  Length:454

    Alignment length:426
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448      
         O53665_MYCTO    29 PQPETLRRYRAGEPPLTGSLLIGGAGRVVEPLRAALEKDYDLVGNNLGGRWADSFGGLVFDATGITEPAGLKGLHEFFTPVLRNLGRCGRVVVVGGTPEAAASTNERIAQRALEGFTRSLGKELRRGATTALVYLSPDAKPAATGLESTMRFLLSAKSAYVDGQVFSVGADDSTPPADWEKPLDGKVAIVTGAARGIGATIAEVFARDGAHVVAIDVESAAENLAETASKVGGTALWLDVTADDAVDKISEHLRDHHGGKADILVNNAGITRDKLLANMDDARWDAVLAVNLLAPLRLTEGLVGNGSIGEGGRVIGLSSIAGIAGNRGQTNYATTKAGMIGITQALAPGLAAKGITINAVAPGFIETQMTAAIPLATREVGRRLNSLLQGGQPVDVAEAIAYFASPASNAVTGNVIRVCGQAMIGA 454
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeeee...hhhhhhhhhh.......-------...eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeeeeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhhh....eeeee..................eeeee...hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......---....hhhhhh.........hhhhhhhhhhhhhh.........eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v1u A  29 PQPETLRRYRAGEPPLTGSLLIGGAGRVVEPLRAALEKDYDLVG-------ADSFGGLVFDATGITEPAGLKGLHEFFTPVLRNLGRCGRVVVVGGTPEAAASTNERIAQRALEGFTRSLGKELRRGATTALVYLSPDAKPAATGLESTMRFLLSAKSAYVDGQVFSVGADDSTPPADWEKPLDGKVAIVTGAARGIGATIAEVFARDGAHVVAIDVESAAENLAETASKVGGTALWLDVTADDAVDKISEHLRDHHGGKADILVNNAGITRDKLLANMDDARWDAVLAVNLLAPLRLTEGLVGNGSIGEGGRVIGLSSIAGIAGNRGQTNYATTKAGMIGITQALAPGLAAKGITINAVAPGFIETQM---IPLATREVGRRLNSLLQGGQPVDVAEAIAYFASPASNAVTGNVIRVCGQAMIGA 454
                                    38        48        58        68   |     - |      88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        |-  |    408       418       428       438       448      
                                                                      72      80                                                                                                                                                                                                                                                                                                                          397 401
   Legend:   → Mismatch (orange background)
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    → 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 3V1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V1U)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (O53665_MYCTO | O53665)
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: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.
    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:0035336    long-chain fatty-acyl-CoA metabolic process    The chemical reactions and pathways involving long-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
    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.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0046459    short-chain fatty acid metabolic process    The chemical reactions and pathways involving fatty acids with a chain length of less than C6.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        O53665_MYCTO | O53665: 3m1l 3q6i 3v1t 4fw8

(-) Related Entries Specified in the PDB File

3lls 3m1l 3q6i 4fw8