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(-) Description

Title :  CRYSTAL STRUCTURE OF CARVEOL DEHYDROGENASE FROM MYCOBACTERIUM THERMORESISTIBILE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  12 Aug 10  (Deposition) - 01 Sep 10  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Haft, P. G. Pierce, S. J. Mayclin, A. Sullivan, A. S. Gardberg, J. Abendroth, D. W. Begley, I. Q. Phan, B. L. Staker, P. J. Myler, V. M. Marathias, D. D. Lorimer, T. E. Edwards
Mycofactocin-Associated Mycobacterial Dehydrogenases With Non-Exchangeable Nad Cofactors.
Sci Rep V. 7 41074 2017
PubMed-ID: 28120876  |  Reference-DOI: 10.1038/SREP41074
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARVEOL DEHYDROGENASE (MYTHA.01326.C, A0R518 HOMOLOG)
    Chains: A, B, C, D
    EC Number: 1.1.1.234
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM THERMORESISTIBILE
    Organism Taxid: 1797
    Strain: ATCC 19527 / NCTC 10409

 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
1NA4Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:250 , THR A:253 , LEU A:255 , HOH A:686BINDING SITE FOR RESIDUE NA A 300
2AC2SOFTWARESER B:250 , THR B:253 , LEU B:255 , HOH B:306BINDING SITE FOR RESIDUE NA B 300
3AC3SOFTWARESER C:250 , THR C:253 , LEU C:255 , ILE C:257 , HOH C:605 , HOH C:736BINDING SITE FOR RESIDUE NA C 300
4AC4SOFTWARESER D:250 , THR D:253 , LEU D:255 , ILE D:257 , HOH D:763 , HOH D:764BINDING SITE FOR RESIDUE NA D 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OEC)

(-) 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:276
 aligned with E1C9L4_MYCTH | E1C9L4 from UniProtKB/TrEMBL  Length:309

    Alignment length:276
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
         E1C9L4_MYCTH    34 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQQPNLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 309
               SCOP domains d3oeca_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhh......hhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oec A  20 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQQPNLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 295
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with E1C9L4_MYCTH | E1C9L4 from UniProtKB/TrEMBL  Length:309

    Alignment length:276
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
         E1C9L4_MYCTH    34 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQQPNLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 309
               SCOP domains d3oecb_ 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.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhh...---hhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oec B  20 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQ--NLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHL---TREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 295
                                    29        39        49        59  |     69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       | - |     249       259       269       279       289      
                                                                  59 62                                                                                                                                                                            237 241                                                      


Chain C from PDB  Type:PROTEIN  Length:274
 aligned with E1C9L4_MYCTH | E1C9L4 from UniProtKB/TrEMBL  Length:309

    Alignment length:276
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
         E1C9L4_MYCTH    34 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQQPNLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 309
               SCOP domains d3oecc_ C: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee....--.......hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhh......hhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oec C  20 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQ--NLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 295
                                    29        39        49        59  |     69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      
                                                                  59 62                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:275
 aligned with E1C9L4_MYCTH | E1C9L4 from UniProtKB/TrEMBL  Length:309

    Alignment length:276
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
         E1C9L4_MYCTH    34 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQQPNLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 309
               SCOP domains d3oecd_ D: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....hhhhhhhhhhhhhh..eeeeee.....-.......hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhh......hhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oec D  20 NRLQGKVAFITGAARGQGRTHAVRLAQDGADIVAIDLCRQQ-NLDYAQGSPEELKETVRLVEEQGRRIIARQADVRDLASLQAVVDEALAEFGHIDILVSNVGISNQGEVVSLTDQQWSDILQTNLIGAWHACRAVLPSMIERGQGGSVIFVSSTVGLRGAPGQSHYAASKHGVQGLMLSLANEVGRHNIRVNSVNPGAVNTEMALNEKLLKMFLPHLENPTREDAAELFSQLTLLPIPWVEPEDVSNAVAWLASDEARYIHGAAIPVDGGQLARA 295
                                    29        39        49        59| |     69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      
                                                                   60 |                                                                                                                                                                                                                                         
                                                                     62
   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 3OEC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (E1C9L4_MYCTH | E1C9L4)
molecular function
    GO:0047890    flavanone 4-reductase activity    Catalysis of the reaction: (2S)-flavan-4-ol + NADP+ = (2S)-flavanone + NADPH.
    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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