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(-) Description

Title :  CRYSTAL STRUCTURE OF MGS-M4, AN ALDO-KETO REDUCTASE ENZYME FROM A MEDEE BASIN DEEP-SEA METAGENOME LIBRARY
 
Authors :  P. J. Stogios, X. Xu, H. Cui, M. Alcaide, M. Ferrer, A. Savchenko
Date :  11 Apr 14  (Deposition) - 25 Feb 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Metagenome, Metagenomic Library, Oxidoreductase, Alpha/Beta Barrel, Tim Barrel, Hydrolase, Unknown Substrate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Alcaide, P. J. Stogios, A. Lafraya, A. Tchigvintsev, R. Flick, R. Bargiela, T. N. Chernikova, O. N. Reva, T. Hai, C. C. Leggewie, N. Katzke, V. La Cono, R. Matesanz, M. Jebbar, K. E. Jaeger, M. M. Yakimov, A. F. Yakunin, P. N. Golyshin, O. V. Golyshina, A. Savchenko, M. Ferrer
Pressure Adaptation Is Linked To Thermal Adaptation In Salt-Saturated Marine Habitats.
Environ Microbiol V. 17 332 2015
PubMed-ID: 25330254  |  Reference-DOI: 10.1111/1462-2920.12660

(-) Compounds

Molecule 1 - MGS-M4
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15-TV LIC
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentMGS-M4
    GeneMGS-M4
    Organism ScientificUNIDENTIFIED
    Organism Taxid32644

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:185 , PRO A:186 , LEU A:187 , MET A:188 , SER A:189 , PRO A:229 , LYS A:230 , HOH A:504 , HOH A:531BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREALA B:185 , PRO B:186 , LEU B:187 , MET B:188 , SER B:189 , PRO B:229 , LYS B:230BINDING SITE FOR RESIDUE SO4 B 301
3AC3SOFTWAREALA C:185 , PRO C:186 , LEU C:187 , MET C:188 , SER C:189 , LYS C:230BINDING SITE FOR RESIDUE SO4 C 301
4AC4SOFTWAREALA D:185 , PRO D:186 , LEU D:187 , MET D:188 , SER D:189 , PRO D:229 , LYS D:230BINDING SITE FOR RESIDUE SO4 D 301
5AC5SOFTWAREALA E:185 , PRO E:186 , LEU E:187 , MET E:188 , SER E:189 , PRO E:229 , LYS E:230 , HOH E:508BINDING SITE FOR RESIDUE SO4 E 301
6AC6SOFTWAREMET F:12 , HIS F:41 , ASP F:43 , THR F:71 , GLU F:182BINDING SITE FOR RESIDUE NA F 301
7AC7SOFTWAREALA F:185 , PRO F:186 , LEU F:187 , MET F:188 , SER F:189 , PRO F:229 , LYS F:230 , HOH F:452 , HOH F:528BINDING SITE FOR RESIDUE SO4 F 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q3M)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q3M)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...ee......hhhhhhhhhhhhhh..eee......hhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3m A   2 HSVKLNNNYEMPIIGLGTFRSKKNDAYNAVKAALEGGYRHIDTAMIYGNEEEVGRAIKDSNIPREEIFVTTKLWNTDQGYEKTLEAFNTSLKNLGLDYIDLYLIHWFKGYDNALSTYRAFETLYEEGKVKAIGVSNFNVHHLMYLMENAKIPPMVNQVETHVTLQNHFLHDYCKKNNIQLEAYAPLMSHQIKDLLSNETMAKIAKKHDKTIPQIAIRWLIEREIVVIPKSITPERIVQNFDVFDFTLDEEDMKSIRSVNTGKKIFTEFDNVDY 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   

Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...ee....hhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3m B   2 HSVKLNNNYEMPIIGLGTFRKNDAYNAVKAALEGGYRHIDTAMIYGNEEEVGRAIKDSNIPREEIFVTTKLWNTDQGYEKTLEAFNTSLKNLGLDYIDLYLIHWFKGYDNALSTYRAFETLYEEGKVKAIGVSNFNVHHLMYLMENAKIPPMVNQVETHVTLQNHFLHDYCKKNNIQLEAYAPLMSHQIKDLLSNETMAKIAKKHDKTIPQIAIRWLIEREIVVIPKSITPERIVQNFDVFDFTLDEEDMKSIRSVNTGKKIFTEFDNVDY 274
                                    11        21|       33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273 
                                              21|                                                                                                                                                                                                                                                          
                                               24                                                                                                                                                                                                                                                          

Chain C from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...ee......hhhhhhhhhhhhhh..eee......hhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3m C   2 HSVKLNNNYEMPIIGLGTFRSKKNDAYNAVKAALEGGYRHIDTAMIYGNEEEVGRAIKDSNIPREEIFVTTKLWNTDQGYEKTLEAFNTSLKNLGLDYIDLYLIHWFKGYDNALSTYRAFETLYEEGKVKAIGVSNFNVHHLMYLMENAKIPPMVNQVETHVTLQNHFLHDYCKKNNIQLEAYAPLMSHQIKDLLSNETMAKIAKKHDKTIPQIAIRWLIEREIVVIPKSITPERIVQNFDVFDFTLDEEDMKSIRSVNTGKKIFTEFDNVDY 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   

Chain D from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...ee......hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3m D   2 HSVKLNNNYEMPIIGLGTFRSKKNDAYNAVKAALEGGYRHIDTAMIYGNEEEVGRAIKDSNIPREEIFVTTKLWNTDQGYEKTLEAFNTSLKNLGLDYIDLYLIHWFKGYDNALSTYRAFETLYEEGKVKAIGVSNFNVHHLMYLMENAKIPPMVNQVETHVTLQNHFLHDYCKKNNIQLEAYAPLMSHQIKDLLSNETMAKIAKKHDKTIPQIAIRWLIEREIVVIPKSITPERIVQNFDVFDFTLDEEDMKSIRSVNTGKKIFTEFDNVDY 274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   

Chain E from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....ee....ee......hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3m E   3 SVKLNNNYEMPIIGLGTFRSKKNDAYNAVKAALEGGYRHIDTAMIYGNEEEVGRAIKDSNIPREEIFVTTKLWNTDQGYEKTLEAFNTSLKNLGLDYIDLYLIHWFKGYDNALSTYRAFETLYEEGKVKAIGVSNFNVHHLMYLMENAKIPPMVNQVETHVTLQNHFLHDYCKKNNIQLEAYAPLMSHQIKDLLSNETMAKIAKKHDKTIPQIAIRWLIEREIVVIPKSITPERIVQNFDVFDFTLDEEDMKSIRSVNTGKKIFTEFDNVDY 274
                                    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 F from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....ee....ee......hhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3m F   2 HSVKLNNNYEMPIIGLGTFRSKKNDAYNAVKAALEGGYRHIDTAMIYGNEEEVGRAIKDSEIFVTTKLWNTDQGYEKTLEAFNTSLKNLGLDYIDLYLIHWFKGYDNALSTYRAFETLYEEGKVKAIGVSNFNVHHLMYLMENAKIPPMVNQVETHVTLQNHFLHDYCKKNNIQLEAYAPLMSHQIKDLLSNETMAKIAKKHDKTIPQIAIRWLIEREIVVIPKSITPERIVQNFDVFDFTLDEEDMKSIRSVNTGKKIFTEFDNVDY 274
                                    11        21        31        41        51        61|       76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        
                                                                                      61|                                                                                                                                                                                                               
                                                                                       67                                                                                                                                                                                                               

   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 4Q3M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q3M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q3M)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Q3M)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4q3k 4q3l 4q3n 4q3o