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(-) Description

Title :  CRYSTAL STRUCTURE OF ENOYL-COA HYDRATASE ECHA16_2 MYCOBACTERIUM PARATUBERCULOSIS ATCC BAA-968 / K-10
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  03 Mar 11  (Deposition) - 16 Mar 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (2x)
Biol. Unit 2:  B,D,F  (2x)
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Lyase (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 - ECHA16_2
    Chains: A, B, C, D, E, F
    EC Number: 4.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ECHA16, MAP_2904
    Organism Scientific: MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS
    Organism Taxid: 1770
    Strain: ATCC BAA-968 / K-10
    Synonym: ENOYL-COA HYDRATASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): A C E 
Biological Unit 2 (2x):  B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:104 , HIS A:124 , PRO A:131 , THR A:132 , TRP A:133 , HOH A:289BINDING SITE FOR RESIDUE EDO A 250
2AC2SOFTWAREGLU B:104 , HIS B:124 , PRO B:131 , THR B:132 , TRP B:133BINDING SITE FOR RESIDUE EDO B 250
3AC3SOFTWARELEU C:65 , GLU C:104 , HIS C:124 , PRO C:131 , THR C:132 , TRP C:133BINDING SITE FOR RESIDUE EDO C 250
4AC4SOFTWAREGLU D:104 , HIS D:124 , PRO D:131 , THR D:132 , TRP D:133 , HOH D:272 , HOH D:278BINDING SITE FOR RESIDUE EDO D 250
5AC5SOFTWARELEU E:65 , GLU E:104 , HIS E:124 , PRO E:131 , THR E:132 , TRP E:133BINDING SITE FOR RESIDUE EDO E 250
6AC6SOFTWAREGLU F:104 , HIS F:124 , PRO F:131 , THR F:132 , TRP F:133BINDING SITE FOR RESIDUE EDO F 250

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:58 -Pro A:59
2Asp B:58 -Pro B:59
3Asp C:58 -Pro C:59
4Asp D:58 -Pro D:59
5Asp E:58 -Pro E:59
6Asp F:58 -Pro F:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QYR)

(-) 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:223
 aligned with Q73VV7_MYCPA | Q73VV7 from UniProtKB/TrEMBL  Length:249

    Alignment length:230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
         Q73VV7_MYCPA     4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKELGGSSALPDISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDDI 233
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..............-------............eeeee..eeehhhhhhhhhh.eeeee...eee............hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyr A   4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKEL-------DISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDDI 233
                                    13        23        33        43        53        63      |  -    |   83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
                                                                                             70      78                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:222
 aligned with Q73VV7_MYCPA | Q73VV7 from UniProtKB/TrEMBL  Length:249

    Alignment length:230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
         Q73VV7_MYCPA     4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKELGGSSALPDISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDDI 233
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..............--------...........eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyr B   4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKEL--------ISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDDI 233
                                    13        23        33        43        53        63      |  -     |  83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
                                                                                             70       79                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:219
 aligned with Q73VV7_MYCPA | Q73VV7 from UniProtKB/TrEMBL  Length:249

    Alignment length:227
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
         Q73VV7_MYCPA     4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKELGGSSALPDISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSG 230
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee...eee........--------...........eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh.....eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyr C   4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKEL--------ISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSG 230
                                    13        23        33        43        53        63      |  -     |  83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
                                                                                             70       79                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:222
 aligned with Q73VV7_MYCPA | Q73VV7 from UniProtKB/TrEMBL  Length:249

    Alignment length:229
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
         Q73VV7_MYCPA     4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKELGGSSALPDISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDD 232
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..............-------............eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhh....eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyr D   4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKEL-------DISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDD 232
                                    13        23        33        43        53        63      |  -    |   83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
                                                                                             70      78                                                                                                                                                          


Chain E from PDB  Type:PROTEIN  Length:220
 aligned with Q73VV7_MYCPA | Q73VV7 from UniProtKB/TrEMBL  Length:249

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q73VV7_MYCPA     4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKELGGSSALPDISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGD 231
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..............--------...........eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh.....eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qyr E   4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKEL--------ISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGD 231
                                    13        23        33        43        53        63      |  -     |  83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                             70       79                                                                                                                                                        


Chain F from PDB  Type:PROTEIN  Length:221
 aligned with Q73VV7_MYCPA | Q73VV7 from UniProtKB/TrEMBL  Length:249

    Alignment length:229
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
         Q73VV7_MYCPA     4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKELGGSSALPDISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDD 232
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---ECH-3qyrF01 F:7-232                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ---ECH-3qyrF02 F:7-232                                                                                                                                                                                                                Pfam domains (2)
           Pfam domains (3) ---ECH-3qyrF03 F:7-232                                                                                                                                                                                                                Pfam domains (3)
           Pfam domains (4) ---ECH-3qyrF04 F:7-232                                                                                                                                                                                                                Pfam domains (4)
           Pfam domains (5) ---ECH-3qyrF05 F:7-232                                                                                                                                                                                                                Pfam domains (5)
           Pfam domains (6) ---ECH-3qyrF06 F:7-232                                                                                                                                                                                                                Pfam domains (6)
         Sec.struct. author ..eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..............--------...........eeeee..eeehhhhhhhhhh.eeeee...eee............hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhh....eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyr F   4 EILLSNTEERVRTLTLNRPQARNALSAALRDRFFGALADAETDDDVDVVIITGADPVFCAGLDLKEL--------ISPRWPALTKPVIGAINGAAVTGGLELALYCDILIASENARFADTHARVGLLPTWGLSVRLPQKVGIGLARRMSLTGDYLSAADALRAGLVTEVVPHDQLLGAAQAVAASIVGNNQNAVRALLASYHRIDDAQTSAGLWQEAMAARQFRTSGDD 232
                                    13        23        33        43        53        63      |  -     |  83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
                                                                                             70       79
   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  (0, 0)

(no "SCOP Domain" information available for 3QYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: ClpP_crotonase (88)
(-)
Family: ECH (52)
(-)
Mycobacterium paratuberculosis (3)
1aECH-3qyrF01F:7-232
1bECH-3qyrF02F:7-232
1cECH-3qyrF03F:7-232
1dECH-3qyrF04F:7-232
1eECH-3qyrF05F:7-232
1fECH-3qyrF06F:7-232

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q73VV7_MYCPA | Q73VV7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
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.

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  3qyr
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 Related Entries

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