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(-) Description

Title :  CRYSTAL STRUCTURE OF SHORT CHAIN DEHYDROGENASE MAP_2410 FROM MYCOBACTERIUM PARATUBERCULOSIS BOUND TO NAD
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  12 Sep 11  (Deposition) - 05 Oct 11  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Oxidoreductase, Nucleotide, Adenine Dinucleotide, Short Chain Dehydrogenase, Srd Family Protein, Carveol Dehydrogenase, Ortholog (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 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: MAP_2410
    Organism Scientific: MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS
    Organism Taxid: 1770

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , ARG A:17 , GLY A:18 , GLN A:19 , ASP A:38 , ILE A:39 , ALA A:52 , VAL A:76 , ASP A:77 , THR A:78 , ASN A:104 , ALA A:105 , GLY A:106 , ILE A:127 , ILE A:155 , SER A:156 , SER A:157 , TYR A:170 , LYS A:174 , PRO A:200 , GLY A:201 , PRO A:202 , VAL A:203 , THR A:205 , PRO A:206 , MET A:207 , HOH A:308 , HOH A:310 , HOH A:349 , HOH A:354BINDING SITE FOR RESIDUE NAD A 274
2AC2SOFTWAREGLY B:14 , ARG B:17 , GLY B:18 , GLN B:19 , ASP B:38 , ILE B:39 , ALA B:52 , VAL B:76 , ASP B:77 , THR B:78 , ASN B:104 , ALA B:105 , GLY B:106 , ILE B:127 , ILE B:155 , SER B:156 , SER B:157 , TYR B:170 , LYS B:174 , PRO B:200 , GLY B:201 , PRO B:202 , VAL B:203 , THR B:205 , PRO B:206 , MET B:207 , HOH B:315 , HOH B:317 , HOH B:327 , HOH B:337BINDING SITE FOR RESIDUE NAD B 274
3AC3SOFTWAREGLY C:14 , ARG C:17 , GLY C:18 , GLN C:19 , ASP C:38 , ILE C:39 , ALA C:52 , VAL C:76 , ASP C:77 , THR C:78 , ASN C:104 , ALA C:105 , GLY C:106 , ILE C:127 , ILE C:155 , SER C:156 , TYR C:170 , LYS C:174 , PRO C:200 , GLY C:201 , PRO C:202 , VAL C:203 , THR C:205 , PRO C:206 , MET C:207 , HOH C:308 , HOH C:313 , HOH C:326 , HOH C:569BINDING SITE FOR RESIDUE NAD C 274
4AC4SOFTWAREGLY D:14 , ARG D:17 , GLY D:18 , GLN D:19 , ASP D:38 , ILE D:39 , VAL D:76 , ASP D:77 , THR D:78 , ASN D:104 , ALA D:105 , GLY D:106 , ILE D:127 , ILE D:155 , SER D:156 , SER D:157 , TYR D:170 , LYS D:174 , PRO D:200 , GLY D:201 , PRO D:202 , VAL D:203 , THR D:205 , PRO D:206 , MET D:207 , HOH D:286 , HOH D:300 , HOH D:371BINDING SITE FOR RESIDUE NAD D 274
5AC5SOFTWAREGLN C:164 , PRO C:165 , LEU C:226 , SER C:227 , LEU C:230BINDING SITE FOR RESIDUE MPD C 275
6AC6SOFTWAREPRO B:54 , LEU B:57 , SER B:58 , VAL B:61 , ALA B:73 , ASP C:82 , HOH C:320BINDING SITE FOR RESIDUE MPD C 276

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TSC)

(-) 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:271
 aligned with Q73X99_MYCPA | Q73X99 from UniProtKB/TrEMBL  Length:273

    Alignment length:271
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 
         Q73X99_MYCPA     3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
               SCOP domains d3tsca_ A: automated matches                                                                                                                                                                                                                                                    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....hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tsc A   3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Q73X99_MYCPA | Q73X99 from UniProtKB/TrEMBL  Length:273

    Alignment length:271
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 
         Q73X99_MYCPA     3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
               SCOP domains d3tscb_ B: automated matches                                                                                                                                                                                                                                                    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....hhhhh.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tsc B   3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 


Chain C from PDB  Type:PROTEIN  Length:271
 aligned with Q73X99_MYCPA | Q73X99 from UniProtKB/TrEMBL  Length:273

    Alignment length:271
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 
         Q73X99_MYCPA     3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
               SCOP domains d3tscc_ C: automated matches                                                                                                                                                                                                                                                    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....hhhhh.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tsc C   3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 


Chain D from PDB  Type:PROTEIN  Length:271
 aligned with Q73X99_MYCPA | Q73X99 from UniProtKB/TrEMBL  Length:273

    Alignment length:271
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 
         Q73X99_MYCPA     3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
               SCOP domains d3tscd_ D: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh.hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tsc D   3 GKLEGRVAFITGAARGQGRAHAVRMAAEGADIIAVDIAGKLPSCVPYDPASPDDLSETVRLVEAANRRIVAAVVDTRDFDRLRKVVDDGVAALGRLDIIVANAGVAAPQAWDDITPEDFRDVMDINVTGTWNTVMAGAPRIIEGGRGGSIILISSAAGMKMQPFMIHYTASKHAVTGLARAFAAELGKHSIRVNSVHPGPVNTPMGSGDMVTAVGQAMETNPQLSHVLTPFLPDWVAEPEDIADTVCWLASDESRKVTAAQIPVDQGSTQY 273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3TSC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q73X99_MYCPA | Q73X99)
molecular function
    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: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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 Related Entries

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(-) Related Entries Specified in the PDB File

3pgx RELATED DEHYDROGENASE FROM M. PARATUBERCULOSIS BOUND TO NAD RELATED ID: MYPAA.01326.G RELATED DB: TARGETDB