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(-) Description

Title :  CRYSTAL STRUCTURE OF ACYL-COA DEHYDROGENASE FROM MYCOBACTERIUM THERMORESISTIBILE BOUND TO FLAVIN ADENINE DINUCLEOTIDE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Jun 10  (Deposition) - 23 Jun 10  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Fad, Fadh, Tuberculosis, Acyl-Coa, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - ACYL-COA DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Organism Scientific: MYCOBACTERIUM THERMORESISTIBILE
    Organism Taxid: 1797

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:129 , LEU A:131 , SER A:132 , GLY A:137 , SER A:138 , TRP A:162 , THR A:164 , ILE A:362 , ILE A:365 , THR A:369 , GLN A:371 , ILE A:372 , HOH A:393 , HOH A:409 , HOH A:419 , HOH A:429 , ARG B:272 , PHE B:275 , ILE B:279 , GLN B:283 , GLN B:340 , VAL B:341 , GLY B:344 , HOH B:453BINDING SITE FOR RESIDUE FAD A 384
2AC2SOFTWAREGLU B:124BINDING SITE FOR RESIDUE NA B 384

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NF4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NF4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NF4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NF4)

(-) Exons   (0, 0)

(no "Exon" information available for 3NF4)

(-) 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:369
 aligned with G7CDN2_MYCT3 | G7CDN2 from UniProtKB/TrEMBL  Length:379

    Alignment length:378
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370        
         G7CDN2_MYCT3     1 MAVDRLLPSQEAAELIELTREIADKVLDPIVDRHEKDETYPEGVFEQLGAAGLLSLPQPEEWGGGGQPYEVYLQVLEEIAARWASVAVAVSVHSLSSHPLLVFGTEEQKKRWLPGMLSGEQIGAYSLSEPQAGSDAAALRCAATPTDGGYVINGSKSWITHGGKADFYTLFARTGEGSRGVSCFLVPADQPGLSFGKPEEKMGLHAVPTTSAFYDNARIDADRRIGEEGQGLQIAFSALDSGRLGIAAVATGLAQAALDEAVAYANERTAFGRKIIDHQGLGFLLADMAAAVATARATYLDAARRRDQGRPYSQQASIAKLTATDAAMKVTTDAVQVFGGVGYTRDYRVERYMREAKIMQIFEGTNQIQRLVIARGLT 378
               SCOP domains d3nf4a1 A:5-232 automated matches                                                                                                                                                                                                   d3nf4a2 A:233-382 automated matches                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhh........hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee........hhhhh..eeeee..eeeeeeeeeeee......eeeeeee..--...eeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------.....-hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nf4 A   5 MAVDRLLPSQEAAELIELTREIADKVLDPIVDRHEKDETYPEGVFEQLGAAGLLSLPQPEEWGGGGQPYEVYLQVLEEIAARWASVAVAVSVHSLSSHPLLVFGTEEQKKRWLPGMLSGEQIGAYSLSEPQAGSDAAALRCAATPTDGGYVINGSKSWITHGGKADFYTLFARTG--SRGVSCFLVPADQPGLSFGKPEEKMGLHAVPTTSAFYDNARIDADRRIGEEGQGLQIAFSALDSGRLGIAAVATGLAQAALDEAVAYANE------KIIDH-GLGFLLADMAAAVATARATYLDAARRRDQGRPYSQQASIAKLTATDAAMKVTTDAVQVFGGVGYTRDYRVERYMREAKIMQIFEGTNQIQRLVIARGLT 382
                                    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       264      |  -   |   284       294       304       314       324       334       344       354       364       374        
                                                                                                                                                                                                        179  |                                                                                      271    278 282 |                                                                                                  
                                                                                                                                                                                                           182                                                                                                   284                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:367
 aligned with G7CDN2_MYCT3 | G7CDN2 from UniProtKB/TrEMBL  Length:379

    Alignment length:378
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370        
         G7CDN2_MYCT3     1 MAVDRLLPSQEAAELIELTREIADKVLDPIVDRHEKDETYPEGVFEQLGAAGLLSLPQPEEWGGGGQPYEVYLQVLEEIAARWASVAVAVSVHSLSSHPLLVFGTEEQKKRWLPGMLSGEQIGAYSLSEPQAGSDAAALRCAATPTDGGYVINGSKSWITHGGKADFYTLFARTGEGSRGVSCFLVPADQPGLSFGKPEEKMGLHAVPTTSAFYDNARIDADRRIGEEGQGLQIAFSALDSGRLGIAAVATGLAQAALDEAVAYANERTAFGRKIIDHQGLGFLLADMAAAVATARATYLDAARRRDQGRPYSQQASIAKLTATDAAMKVTTDAVQVFGGVGYTRDYRVERYMREAKIMQIFEGTNQIQRLVIARGLT 378
               SCOP domains d3nf4b1 B:5-232 automated matches                                                                                                                                                                                                   d3nf4b2 B:233-382 automated matches                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhh.......hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....---------..eeeee..eeeeeeeeeeee......eeeeeee.--....eeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nf4 B   5 MAVDRLLPSQEAAELIELTREIADKVLDPIVDRHEKDETYPEGVFEQLGAAGLLSLPQPEEWGGGGQPYEVYLQVLEEIAARWASVAVAVSVHSLSSHPLLVFGTEEQKKRWLPGMLSGEQIGAYSLSEP---------RCAATPTDGGYVINGSKSWITHGGKADFYTLFART--GSRGVSCFLVPADQPGLSFGKPEEKMGLHAVPTTSAFYDNARIDADRRIGEEGQGLQIAFSALDSGRLGIAAVATGLAQAALDEAVAYANERTAFGRKIIDHQGLGFLLADMAAAVATARATYLDAARRRDQGRPYSQQASIAKLTATDAAMKVTTDAVQVFGGVGYTRDYRVERYMREAKIMQIFEGTNQIQRLVIARGLT 382
                                    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       264       274       284       294       304       314       324       334       344       354       364       374        
                                                                                                                                                           134       144                               178  |                                                                                                                                                                                                         
                                                                                                                                                                                                          181
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NF4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NF4)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (G7CDN2_MYCT3 | G7CDN2)
molecular function
    GO:0003995    acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
    GO:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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