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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF FATTY ALDEHYDE DEHYDROGENASE ENZYMES FROM MARINOBACTER AQUAEOLEI VT8 COMPLEXED WITH A SUBSTRATE
 
Authors :  K. Shi, K. Mulliner, B. M. Barney, H. Aihara
Date :  24 Nov 16  (Deposition) - 26 Apr 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Bertram, K. M. Mulliner, K. Shi, M. H. Plunkett, P. Nixon, N. A. Serratore, C. J. Douglas, H. Aihara, B. M. Barney
Five Fatty Aldehyde Dehydrogenase Enzymes From Marinobacter And Acinetobacter Spp. And Structural Insights Into The Aldehyde Binding Pocket.
Appl. Environ. Microbiol. V. 83 2017
PubMed-ID: 28389542  |  Reference-DOI: 10.1128/AEM.00018-17

(-) Compounds

Molecule 1 - N-SUCCINYLGLUTAMATE 5-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.71
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ASTD, MAQU_3316
    Organism Scientific: MARINOBACTER HYDROCARBONOCLASTICUS (STRAIN ATCC 700491 / DSM 11845 / VT8)
    Organism Taxid: 351348
    Strain: ATCC 700491 / DSM 11845 / VT8
    Synonym: SUCCINYLGLUTAMIC SEMIALDEHYDE DEHYDROGENASE,SGSD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
18YP1Ligand/IonDECANAL
2CL1Ligand/IonCHLORIDE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:393 , ASP A:394 , ARG A:421binding site for residue EDO A 501
02AC2SOFTWAREGLY A:147 , LYS A:173 , PRO A:174 , SER A:175 , GLU A:176 , EDO A:508 , HOH A:622binding site for residue EDO A 502
03AC3SOFTWARESER A:441 , SER A:442 , HOH A:608 , VAL B:128binding site for residue EDO A 503
04AC4SOFTWAREHIS A:123 , ARG A:136 , ARG A:138binding site for residue EDO A 504
05AC5SOFTWAREASN A:252 , ARG A:287 , GLU A:376 , TYR A:388 , ASN A:402binding site for residue EDO A 505
06AC6SOFTWAREPRO A:457 , TYR A:461 , ASP A:464 , ASP B:464 , PRO B:469binding site for residue EDO A 506
07AC7SOFTWARELYS A:109 , HIS A:154 , LEU A:155 , GLY A:158 , HIS A:159 , THR A:224 , SER A:458 , ALA A:459binding site for residue 8YP A 507
08AC8SOFTWARESER A:206 , EDO A:502binding site for residue EDO A 508
09AC9SOFTWARECYS A:282 , THR A:283 , THR A:438binding site for residue EDO A 509
10AD1SOFTWAREGLN B:258 , PHE B:393 , ARG B:421binding site for residue MPD B 501
11AD2SOFTWAREHIS A:234 , ASN A:454 , ARG A:456 , LEU B:245 , ARG B:456binding site for residue MPD B 502
12AD3SOFTWAREARG B:138binding site for residue CL B 503
13AD4SOFTWAREASP A:359 , ARG A:416 , GLU B:125 , GLU B:474binding site for residue PO4 B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U0L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U0L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U0L)

(-) Exons   (0, 0)

(no "Exon" information available for 5U0L)

(-) 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:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh......eee...hhhhhhhhhh.....eeeee.hhhhhhhhhhhh......eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh..eeee..............eeee..............eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee...........ee..hhhhh....ee.hhhhhheeeeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u0l A   3 NLTGNVYIDGLWLPGHGAPFESVQPVTGETVWDGNAASLEDVDAAVREARKAFLAWRRKSLAERQAVIEAFGELLEANKEELAHQIGLETGKPLWESRTEVAAMMGKIPISVKAYNERTGHTESDVAGGHAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPGVAELTVRLWEKAGLPDGVINLVQGGSDTGKCLARHSLIDGLFFTGSSTVGHLLHEQFGGQPEKILALEMGGNNPLIVQNVSDLDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDEFLARLVEVAARITVAEFDADPQPFMGSVISAEAANQLLKAQAAMLEKGATSLLEMKQLKPDTGLLSPGIVDATGIELEDQEFFGPLLTVYRYKGFDEALELANNTRYGLSAGILSDDRKLYNRLVEEVRAGIVNWNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSELPDSLAPGLNF 490
                                    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       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482        


Chain B from PDB  Type:PROTEIN  Length:487
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh......eee...hhhhhhhhhh.....eeeee.hhhhhhhhhhhh......eeeee....eeeee....hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh..eeee..............eeee..............eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee...........ee..hhhhh....ee.hhhhhheeeeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u0l B   4 LTGNVYIDGLWLPGHGAPFESVQPVTGETVWDGNAASLEDVDAAVREARKAFLAWRRKSLAERQAVIEAFGELLEANKEELAHQIGLETGKPLWESRTEVAAMMGKIPISVKAYNERTGHTESDVAGGHAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPGVAELTVRLWEKAGLPDGVINLVQGGSDTGKCLARHSLIDGLFFTGSSTVGHLLHEQFGGQPEKILALEMGGNNPLIVQNVSDLDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDEFLARLVEVAARITVAEFDADPQPFMGSVISAEAANQLLKAQAAMLEKGATSLLEMKQLKPDTGLLSPGIVDATGIELEDQEFFGPLLTVYRYKGFDEALELANNTRYGLSAGILSDDRKLYNRLVEEVRAGIVNWNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSELPDSLAPGLNF 490
                                    13        23        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       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5U0L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U0L)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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