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(-) Description

Title :  CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH SHOWING A THIOHEMIACETAL WITH BETAINE ALDEHYDE
 
Authors :  A. Zarate-Romero, R. A. Munoz-Clares
Date :  18 Oct 14  (Deposition) - 20 Jan 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxidoreductase, Betaine Aldehyde Dehydrogenase, Aldh10. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Zarate-Romero, D. S. Murillo-Melo, C. Mujica-Jimenez, C. Montiel R. A. Munoz-Clares
Reversible, Partial Inactivation Of Plant Betaine Aldehyde Dehydrogenase By Betaine Aldehyde: Mechanism And Possible Physiological Implications.
Biochem. J. V. 473 873 2016
PubMed-ID: 26792760  |  Reference-DOI: 10.1042/BJ20151084

(-) Compounds

Molecule 1 - BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
    Chains: A, B, D
    EC Number: 1.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562
    Synonym: BADH, BETAINE ALDEHYDE DEHYDROGENASE
 
Molecule 2 - BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
    Chains: C
    EC Number: 1.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562
    Synonym: BADH, BETAINE ALDEHYDE DEHYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 29)

Asymmetric Unit (6, 29)
No.NameCountTypeFull Name
1CHT3Ligand/IonCHOLINE ION
2CSO5Mod. Amino AcidS-HYDROXYCYSTEINE
3ETX1Ligand/Ion2-ETHOXYETHANOL
4GOL2Ligand/IonGLYCEROL
5IOD15Ligand/IonIODIDE ION
6PG43Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (5, 15)
No.NameCountTypeFull Name
1CHT2Ligand/IonCHOLINE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3ETX-1Ligand/Ion2-ETHOXYETHANOL
4GOL1Ligand/IonGLYCEROL
5IOD9Ligand/IonIODIDE ION
6PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (6, 14)
No.NameCountTypeFull Name
1CHT1Ligand/IonCHOLINE ION
2CSO3Mod. Amino AcidS-HYDROXYCYSTEINE
3ETX1Ligand/Ion2-ETHOXYETHANOL
4GOL1Ligand/IonGLYCEROL
5IOD6Ligand/IonIODIDE ION
6PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:143 , THR B:434BINDING SITE FOR RESIDUE IOD A1499
02AC2SOFTWARELYS A:21 , ASN A:23BINDING SITE FOR RESIDUE IOD A1500
03AC3SOFTWAREGLN A:474BINDING SITE FOR RESIDUE IOD A1501
04AC4SOFTWARETYR A:160 , TRP A:167 , ILE A:290 , SER A:292 , GLN A:448 , CYS A:450BINDING SITE FOR RESIDUE CHT A1502
05AC5SOFTWARETRP A:471 , GLN A:474 , GLU B:470 , TRP B:471BINDING SITE FOR RESIDUE PG4 A1503
06AC6SOFTWAREGLU A:431 , HIS B:143BINDING SITE FOR RESIDUE IOD B1498
07AC7SOFTWARELYS B:128BINDING SITE FOR RESIDUE IOD B1499
08AC8SOFTWAREHOH A:2186 , GLY B:465BINDING SITE FOR RESIDUE IOD B1500
09AC9SOFTWARETYR B:160 , TRP B:167 , CSO B:291 , GLN B:448 , CYS B:450BINDING SITE FOR RESIDUE CHT B1501
10BC1SOFTWARECYS B:450 , PHE B:451 , HOH B:2121BINDING SITE FOR RESIDUE GOL B1502
11BC2SOFTWAREHIS C:143BINDING SITE FOR RESIDUE IOD C1498
12BC3SOFTWAREGLN C:474BINDING SITE FOR RESIDUE IOD C1499
13BC4SOFTWARETRP C:471 , GLU D:470 , TRP D:471BINDING SITE FOR RESIDUE PG4 C1500
14BC5SOFTWARETHR C:378 , ASP C:379 , ILE C:380 , VAL C:398 , HOH C:2128BINDING SITE FOR RESIDUE ETX C1501
15BC6SOFTWARETHR C:434 , LYS D:130 , HIS D:143BINDING SITE FOR RESIDUE IOD D1498
16BC7SOFTWAREARG D:146BINDING SITE FOR RESIDUE IOD D1500
17BC8SOFTWARETYR D:160 , ILE D:290 , CSO D:291 , GLN D:448 , CYS D:450BINDING SITE FOR RESIDUE CHT D1501
18BC9SOFTWARELEU C:149 , VAL C:251 , PRO C:253 , LEU C:477 , ILE C:479 , GLY D:458 , ILE D:459 , LYS D:460 , GLY D:463 , PHE D:464 , ARG D:466 , HOH D:2170BINDING SITE FOR RESIDUE PG4 D1502
19CC1SOFTWAREPHE D:281 , TRP D:285 , GLN D:448 , PRO D:449 , CYS D:450 , HOH D:2177BINDING SITE FOR RESIDUE GOL D1503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V3F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V3F)

(-) Exons   (0, 0)

(no "Exon" information available for 4V3F)

(-) 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:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh......eee...hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeee....eeeee....hhhhhhhhhhhh.hhhhhh.....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3f A   3 FPIPARQLFIDGEWREPIKKNRIPVINPSTEEIIGDIPAATAEDVEVAVVAARRAFRRNNWSATSGAHRATYLRAIAAKITEKKDHFVKLETIDSGKPFDEAVLDIDDVASCFEYFAGQAEALDGKQKAPVTLPMERFKSHVLRQPLGVVGLISPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLEFGEVCNEVGLPPGVLNILTGLGPDAGAPLVSHPDVDKIAFTGSSATGSKVMASAAQLVKPVTLELGGKSPIVVFEDVDIDKVVEWTIFGCFWTNGQIcCSATSRLLVHESIAAEFVDKLVKWTKNIKISDPFEEGCRLGPVISKGQYDKIMKFISTAKSEGATILYGGSRPEHLKKGYYIEPTIVTDISTSMQIWKEEVFGPVLCVKTFSSEDEAIALANDTEYGLAAAVFSNDLERCERITKALEVGAVWVNCSQPCFVQAPWGGIKRSGFGRELGEWGIQNYLNIKQVTQDISDEPWGWYKSP 497
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491      
                                                                                                                                                                                                                                                                                                                          291-CSO                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh....eeee....eeeee....hhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3f B   4 PIPARQLFIDGEWREPIKKNRIPVINPSTEEIIGDIPAATAEDVEVAVVAARRAFRRNNWSATSGAHRATYLRAIAAKITEKKDHFVKLETIDSGKPFDEAVLDIDDVASCFEYFAGQAEALDGKQKAPVTLPMERFKSHVLRQPLGVVGLISPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLEFGEVCNEVGLPPGVLNILTGLGPDAGAPLVSHPDVDKIAFTGSSATGSKVMASAAQLVKPVTLELGGKSPIVVFEDVDIDKVVEWTIFGCFWTNGQIcCSATSRLLVHESIAAEFVDKLVKWTKNIKISDPFEEGCRLGPVISKGQYDKIMKFISTAKSEGATILYGGSRPEHLKKGYYIEPTIVTDISTSMQIWKEEVFGPVLCVKTFSSEDEAIALANDTEYGLAAAVFSNDLERCERITKALEVGAVWVNCSQPCFVQAPWGGIKRSGFGRELGEWGIQNYLNIKQVTQDISDEPWGWYKSP 497
                                    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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492     
                                                                                                                                                                                                                                                                                                                         291-CSO                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhh......eee...hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh....eeee.....eeee....hhhhhhhhhhhh.hhhhhh......eeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3f C   3 FPIPARQLFIDGEWREPIKKNRIPVINPSTEEIIGDIPAATAEDVEVAVVAARRAFRRNNWSATSGAHRATYLRAIAAKITEKKDHFVKLETIDSGKPFDEAVLDIDDVASCFEYFAGQAEALDGKQKAPVTLPMERFKSHVLRQPLGVVGLISPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLEFGEVCNEVGLPPGVLNILTGLGPDAGAPLVSHPDVDKIAFTGSSATGSKVMASAAQLVKPVTLELGGKSPIVVFEDVDIDKVVEWTIFGCFWTNGQIcSATSRLLVHESIAAEFVDKLVKWTKNIKISDPFEEGCRLGPVISKGQYDKIMKFISTAKSEGATILYGGSRPEHLKKGYYIEPTIVTDISTSMQIWKEEVFGPVLCVKTFSSEDEAIALANDTEYGLAAAVFSNDLERCERITKALEVGAVWVNCSQPcFVQAPWGGIKRSGFGRELGEWGIQNYLNIKQVTQDISDEPWGWYKSP 497
                                    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       492     
                                                                                                                                                                                                                                                                                                                          291-CSO                                                                                                                                                        450-CSO                                           


Chain D from PDB  Type:PROTEIN  Length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeee..eeeeee...hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh......eee.......hhhhhhhh....eeeee.hhhhhhhhhhhhhhh...eeee....eeeee....hhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3f D   3 FPIPARQLFIDGEWREPIKKNRIPVINPSTEEIIGDIPAATAEDVEVAVVAARRAFRRNNWSATSGAHRATYLRAIAAKITEKKDHFVKLETIDSGKPFDEAVLDIDDVASCFEYFAGQAEALDGKQKAPVTLPMERFKSHVLRQPLGVVGLISPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLEFGEVCNEVGLPPGVLNILTGLGPDAGAPLVSHPDVDKIAFTGSSATGSKVMASAAQLVKPVTLELGGKSPIVVFEDVDIDKVVEWTIFGCFWTNGQIcCSATSRLLVHESIAAEFVDKLVKWTKNIKISDPFEEGCRLGPVISKGQYDKIMKFISTAKSEGATILYGGSRPEHLKKGYYIEPTIVTDISTSMQIWKEEVFGPVLCVKTFSSEDEAIALANDTEYGLAAAVFSNDLERCERITKALEVGAVWVNCSQPCFVQAPWGGIKRSGFGRELGEWGIQNYLNIKQVTQDISDEPWGWYKSP 497
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491      
                                                                                                                                                                                                                                                                                                                          291-CSO
   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)

(no "SCOP Domain" information available for 4V3F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V3F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V3F)

(-) Gene Ontology  (10, 10)

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  BADH_SPIOL | P17202
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        BADH_SPIOL | P17202: 4a0m 4v37 5a2d

(-) Related Entries Specified in the PDB File

4v37 CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH SHOWING A THIOHEMIACETAL WITH 3- AMINOPROPIONALDEHYDE