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(-) Description

Title :  1.90 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF APO BETAINE ALDEHYDE DEHYDROGENASE (BETB) G234S MUTANT FROM STAPHYLOCOCCUS AUREUS (IDP00699) WITH BME-MODIFIED CYS289
 
Authors :  A. S. Halavaty, G. Minasov, C. Chen, J. C. Joo, A. F. Yakunin, W. F. Anders For Structural Genomics Of Infectious Diseases (Csgid)
Date :  28 Apr 14  (Deposition) - 07 May 14  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Structural Genomics, Nad, Center For Structural Genomics Of Infectious, Niaid, National Institute Of Allergy And Infectious Diseases, Csgid, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, R. L. Rich, C. Chen, J. C. Joo, G. Minasov, I. Dubrovska, J. R. Winsor, D. G. Myszka, M. Duban, L. Shuvalova, A. F. Yakunin, W. F. Anderson
Structural And Functional Analysis Of Betaine Aldehyde Dehydrogenase From Staphylococcus Aureus.
Acta Crystallogr. , Sect. D V. 71 1159 2015
PubMed-ID: 25945581  |  Reference-DOI: 10.1107/S1399004715004228

(-) Compounds

Molecule 1 - BETAINE ALDEHYDE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV-LIC
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: BETB, SACOL2628
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 93062
    Strain: COL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2NA6Ligand/IonSODIUM ION
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2NA-1Ligand/IonSODIUM ION
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2NA-1Ligand/IonSODIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2NA-1Ligand/IonSODIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:286 , GLU A:390 , GLY A:393 , HOH A:644 , HOH A:785 , HOH A:956BINDING SITE FOR RESIDUE NA A 501
2AC2SOFTWARELYS A:460 , GLY A:463 , HOH A:690 , VAL B:249 , HOH B:912BINDING SITE FOR RESIDUE NA A 502
3AC3SOFTWAREARG A:77 , ASP A:81 , ASP D:81BINDING SITE FOR RESIDUE PEG A 503
4AC4SOFTWAREVAL A:249 , HOH A:978 , LYS B:460 , GLY B:463 , HOH B:699BINDING SITE FOR RESIDUE NA B 501
5AC5SOFTWARELYS C:460 , GLY C:463 , HOH C:646 , VAL D:249 , HOH D:645BINDING SITE FOR RESIDUE NA C 501
6AC6SOFTWAREGLY C:286 , SER C:293 , GLY C:393 , HOH C:651 , HOH C:1001 , HOH C:1030BINDING SITE FOR RESIDUE NA C 502
7AC7SOFTWAREASP B:81 , ASP C:81BINDING SITE FOR RESIDUE PEG C 503
8AC8SOFTWAREVAL C:249 , HOH C:662 , LYS D:460 , GLY D:463 , HOH D:608BINDING SITE FOR RESIDUE NA D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q92)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q92)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q92)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q92)

(-) 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:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.....eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh..eeee..................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q92 A   0 GMELLKHLSQRQYIDGEWVESANKNTRDIINPYNQEVIFTVSEGTKEDAERAILAARRAFESGEWSQETAETRGKKVRAIADKIKEHREALARLETLDTGKTLEESYADMDDIHNVFMYFAGLADKDGGEMIDSPIPDTESKIVKEPVGVVTQITPWNYPLLQASWKIAPALATGCSLVMKPSEITPLTTIRVFELMEEVGFPKGTINLILGAGSEVGDVMSGHKEVDLVSFTGSIETGKHIMKNAANNVTNIALELGGKNPNIIFDDADFELAVDQALNGGYFHAGQVcSAGSRILVQNSIKDKFEQALIDRVKKIKLGNGFDADTEMGPVISTEHRNKIESYMDVAKAEGATIAVGGKRPDRDDLKDGLFFEPTVITNCDTSMRIVQEEVFGPVVTVEGFETEQEAIQLANDSIYGLAGAVFSKDIGKAQRVANKLKLGTVWINDFHPYFAQAPWGGYKQSGIGRELGKEGLEEYLVSKHILTNTNPQLVNWFSK 496
                                     9        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       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       
                                                                                                                                                                                                                                                                                                                           289-CME                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.....eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh..eeee..................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q92 B   0 GMELLKHLSQRQYIDGEWVESANKNTRDIINPYNQEVIFTVSEGTKEDAERAILAARRAFESGEWSQETAETRGKKVRAIADKIKEHREALARLETLDTGKTLEESYADMDDIHNVFMYFAGLADKDGGEMIDSPIPDTESKIVKEPVGVVTQITPWNYPLLQASWKIAPALATGCSLVMKPSEITPLTTIRVFELMEEVGFPKGTINLILGAGSEVGDVMSGHKEVDLVSFTGSIETGKHIMKNAANNVTNIALELGGKNPNIIFDDADFELAVDQALNGGYFHAGQVcSAGSRILVQNSIKDKFEQALIDRVKKIKLGNGFDADTEMGPVISTEHRNKIESYMDVAKAEGATIAVGGKRPDRDDLKDGLFFEPTVITNCDTSMRIVQEEVFGPVVTVEGFETEQEAIQLANDSIYGLAGAVFSKDIGKAQRVANKLKLGTVWINDFHPYFAQAPWGGYKQSGIGRELGKEGLEEYLVSKHILTNTNPQLVNWFSK 496
                                     9        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       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       
                                                                                                                                                                                                                                                                                                                           289-CME                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.....eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh..eeee..................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q92 C   1 MELLKHLSQRQYIDGEWVESANKNTRDIINPYNQEVIFTVSEGTKEDAERAILAARRAFESGEWSQETAETRGKKVRAIADKIKEHREALARLETLDTGKTLEESYADMDDIHNVFMYFAGLADKDGGEMIDSPIPDTESKIVKEPVGVVTQITPWNYPLLQASWKIAPALATGCSLVMKPSEITPLTTIRVFELMEEVGFPKGTINLILGAGSEVGDVMSGHKEVDLVSFTGSIETGKHIMKNAANNVTNIALELGGKNPNIIFDDADFELAVDQALNGGYFHAGQVcSAGSRILVQNSIKDKFEQALIDRVKKIKLGNGFDADTEMGPVISTEHRNKIESYMDVAKAEGATIAVGGKRPDRDDLKDGLFFEPTVITNCDTSMRIVQEEVFGPVVTVEGFETEQEAIQLANDSIYGLAGAVFSKDIGKAQRVANKLKLGTVWINDFHPYFAQAPWGGYKQSGIGRELGKEGLEEYLVSKHILTNTNPQLVNWFSK 496
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490      
                                                                                                                                                                                                                                                                                                                          289-CME                                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.....eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh..eeee..................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q92 D  -4 LYFQGMELLKHLSQRQYIDGEWVESANKNTRDIINPYNQEVIFTVSEGTKEDAERAILAARRAFESGEWSQETAETRGKKVRAIADKIKEHREALARLETLDTGKTLEESYADMDDIHNVFMYFAGLADKDGGEMIDSPIPDTESKIVKEPVGVVTQITPWNYPLLQASWKIAPALATGCSLVMKPSEITPLTTIRVFELMEEVGFPKGTINLILGAGSEVGDVMSGHKEVDLVSFTGSIETGKHIMKNAANNVTNIALELGGKNPNIIFDDADFELAVDQALNGGYFHAGQVcSAGSRILVQNSIKDKFEQALIDRVKKIKLGNGFDADTEMGPVISTEHRNKIESYMDVAKAEGATIAVGGKRPDRDDLKDGLFFEPTVITNCDTSMRIVQEEVFGPVVTVEGFETEQEAIQLANDSIYGLAGAVFSKDIGKAQRVANKLKLGTVWINDFHPYFAQAPWGGYKQSGIGRELGKEGLEEYLVSKHILTNTNPQLVNWFSK 496
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   |   295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495 
                                                                                                                                                                                                                                                                                                                               289-CME
   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  (0, 0)

(no "SCOP Domain" information available for 4Q92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q92)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Q92)

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  4q92
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 Related Entries

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

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        A0A0H2X0S3_S | A0A0H2X0S3: 4mpb 4mpy 4nea 4nu9 4qje 4qn2

(-) Related Entries Specified in the PDB File

4mpb 1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE (BETB) FROM STAPHYLOCOCCUS AUREUS
4mpy 1.85 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE (BETB) FROM STAPHYLOCOCCUS AUREUS (IDP00699) IN COMPLEX WITH NAD+
4nea 1.90 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE (BETB) FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH NAD+ AND BME-FREE CYS289
4ni4 2.6 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE (BETB) G234S MUTANT FROM STAPHYLOCOCCUS AUREUS (IDP00699) IN COMPLEX WITH NAD+ AND BME-FREE CYS289
4nu9 2.30 ANGSTROM RESOLUTION CRYSTAL STRUCURE OF BETAINE ALDEHYDE DEHYDROGENASE (BETB) FROM STAPHYLOCOCCUS AUREUS WITH BME-FREE CYS289 RELATED ID: CSGID-IDP00699 RELATED DB: TARGETTRACK