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(-) Description

Title :  CRYSTAL STRUCTURE OF CARVEOL DEHYDROGENASE FROM MYCOBACTERIUM AVIUM IN COMPLEX WITH NAD
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  31 Oct 15  (Deposition) - 02 Dec 15  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Ssgcid, Carveol Dehydrogenase, Nad, Dehydrogenase, Mycobacterium Avium, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, 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
    Chains: A, B, C, D
    EC Number: 1.1.1.275
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MYAVA.01326.Q.A1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MAV_2983
    Organism Scientific: MYCOBACTERIUM AVIUM
    Organism Taxid: 243243
    Strain: 104
    Synonym: MYAVA.01326.Q

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:22 , ARG A:25 , GLY A:26 , GLN A:27 , ASP A:46 , ILE A:47 , ILE A:51 , SER A:59 , VAL A:83 , ASP A:84 , VAL A:85 , ASN A:111 , ALA A:112 , GLY A:113 , VAL A:114 , ILE A:135 , THR A:163 , SER A:164 , SER A:165 , TYR A:178 , LYS A:182 , PRO A:208 , THR A:209 , GLN A:210 , VAL A:211 , THR A:213 , MET A:215 , VAL A:216 , HOH A:403 , HOH A:405 , HOH A:425 , HOH A:464 , HOH A:494binding site for residue NAD A 300
02AC2SOFTWAREARG A:169 , ARG A:190 , HOH A:462 , ARG B:169 , ARG B:190binding site for residue PO4 A 301
03AC3SOFTWARETYR A:172 , PRO A:173binding site for residue MPD A 302
04AC4SOFTWAREGLY B:22 , ARG B:25 , GLY B:26 , GLN B:27 , ASP B:46 , ILE B:47 , ILE B:51 , SER B:59 , VAL B:83 , ASP B:84 , VAL B:85 , ASN B:111 , ALA B:112 , GLY B:113 , VAL B:114 , ILE B:135 , THR B:163 , SER B:164 , SER B:165 , TYR B:178 , LYS B:182 , PRO B:208 , THR B:209 , GLN B:210 , VAL B:211 , THR B:213 , MET B:215 , VAL B:216 , HOH B:407 , HOH B:414 , HOH B:425 , HOH B:468 , HOH B:485binding site for residue NAD B 301
05AC5SOFTWARETYR B:172 , PRO B:173binding site for residue MPD B 302
06AC6SOFTWAREGLY C:22 , ARG C:25 , GLY C:26 , GLN C:27 , ASP C:46 , ILE C:47 , ILE C:51 , SER C:59 , VAL C:83 , ASP C:84 , VAL C:85 , ASN C:111 , ALA C:112 , GLY C:113 , VAL C:114 , ILE C:135 , THR C:163 , SER C:164 , SER C:165 , TYR C:178 , LYS C:182 , PRO C:208 , THR C:209 , GLN C:210 , VAL C:211 , THR C:213 , MET C:215 , VAL C:216 , HOH C:403 , HOH C:411 , HOH C:415 , HOH C:454 , HOH C:470binding site for residue NAD C 301
07AC7SOFTWARETYR C:172 , PRO C:173binding site for residue MPD C 302
08AC8SOFTWAREARG C:169 , ARG C:190 , HOH C:402 , ARG D:169 , ARG D:190binding site for residue PO4 C 303
09AC9SOFTWAREGLY D:22 , ARG D:25 , GLY D:26 , GLN D:27 , ASP D:46 , ILE D:47 , ILE D:51 , SER D:59 , VAL D:83 , ASP D:84 , VAL D:85 , ASN D:111 , ALA D:112 , GLY D:113 , VAL D:114 , ILE D:135 , THR D:163 , SER D:164 , SER D:165 , TYR D:178 , LYS D:182 , PRO D:208 , THR D:209 , GLN D:210 , VAL D:211 , THR D:213 , MET D:215 , VAL D:216 , HOH D:402 , HOH D:418 , HOH D:429 , HOH D:431 , HOH D:442binding site for residue NAD D 301
10AD1SOFTWARETYR D:172 , PRO D:173binding site for residue MPD D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EJ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5EJ2)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh......hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ej2 A  10 TGRVAGKVAFISGAARGQGRSHAVRLAQEGADIIAIDICGPIENLAYPHSTPEDLAETADLVKDLDRRIVTAQVDVRDFEALKSAVDSGVEQLGRLDIIVANAGVGTDGRKLHKIRDNVWQDMIDINLTGVWHTVKAGVPHVLSGGRGGSIVLTSSVGGRKAYPNTGHYIAAKHGVIGLMRAFAVELGPHMIRVNAVLPTQVSTTMVMNDQTFRLFRPDLENPGPDDFAPISQMMHTLPVPWVDASDISNAVLFLASDESRYVTGVSLPVDAGSLLK 286
                                    19        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       


Chain B from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh......hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ej2 B  10 TGRVAGKVAFISGAARGQGRSHAVRLAQEGADIIAIDICGPIENLAYPHSTPEDLAETADLVKDLDRRIVTAQVDVRDFEALKSAVDSGVEQLGRLDIIVANAGVGTDGRKLHKIRDNVWQDMIDINLTGVWHTVKAGVPHVLSGGRGGSIVLTSSVGGRKAYPNTGHYIAAKHGVIGLMRAFAVELGPHMIRVNAVLPTQVSTTMVMNDQTFRLFRPDLENPGPDDFAPISQMMHTLPVPWVDASDISNAVLFLASDESRYVTGVSLPVDAGSLLK 286
                                    19        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       


Chain C from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh......hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ej2 C  10 TGRVAGKVAFISGAARGQGRSHAVRLAQEGADIIAIDICGPIENLAYPHSTPEDLAETADLVKDLDRRIVTAQVDVRDFEALKSAVDSGVEQLGRLDIIVANAGVGTDGRKLHKIRDNVWQDMIDINLTGVWHTVKAGVPHVLSGGRGGSIVLTSSVGGRKAYPNTGHYIAAKHGVIGLMRAFAVELGPHMIRVNAVLPTQVSTTMVMNDQTFRLFRPDLENPGPDDFAPISQMMHTLPVPWVDASDISNAVLFLASDESRYVTGVSLPVDAGSLLK 286
                                    19        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       


Chain D from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh......hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ej2 D  10 TGRVAGKVAFISGAARGQGRSHAVRLAQEGADIIAIDICGPIENLAYPHSTPEDLAETADLVKDLDRRIVTAQVDVRDFEALKSAVDSGVEQLGRLDIIVANAGVGTDGRKLHKIRDNVWQDMIDINLTGVWHTVKAGVPHVLSGGRGGSIVLTSSVGGRKAYPNTGHYIAAKHGVIGLMRAFAVELGPHMIRVNAVLPTQVSTTMVMNDQTFRLFRPDLENPGPDDFAPISQMMHTLPVPWVDASDISNAVLFLASDESRYVTGVSLPVDAGSLLK 286
                                    19        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
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0 ; only for superseded entry 3UWR: 1,4)

(no "SCOP Domain" information available for 5EJ2, only for superseded entry 3UWR replaced by 5EJ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EJ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EJ2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  5ej2
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