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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ALDEHYDE DEHYDROGENASE FROM SINORHIZOBIUM MELILOTI 1021 COMPLEXED WITH NAD
 
Authors :  V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garfo A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. L A. Celikgil, G. Villegas, B. Evans, W. Zenchek, J. Love, A. Fiser, K. Kh R. Seidel, J. B. Bonanno, S. C. Almo, New York Structural Genomics Consortium (Nysgrc)
Date :  09 May 12  (Deposition) - 30 May 12  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
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, Protein Structure Initiative, Nysgrc, Psi- Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. Lim, A. Celikgil, G. Villegas, B. Evans, W. Zenchek, J. Love, A. Fiser, K. Khafizov, R. Seidel, J. B. Bonanno, S. C. Almo
Crystal Structure Of Putative Aldehyde Dehydrogenase From Sinorhizobium Meliloti 1021 Complexed With Nad
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ALDEHYDE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: R02268, SMC01656
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 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, 56)

Asymmetric Unit (3, 56)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MSE47Mod. Amino AcidSELENOMETHIONINE
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (3, 56)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MSE47Mod. Amino AcidSELENOMETHIONINE
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (3, 29)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE24Mod. Amino AcidSELENOMETHIONINE
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (3, 27)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE23Mod. Amino AcidSELENOMETHIONINE
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:145 , ALA A:146 , PRO A:147 , TRP A:148 , LYS A:172 , SER A:174 , GLU A:175 , GLY A:204 , GLY A:208 , ASN A:209 , ILE A:212 , ILE A:222 , THR A:223 , GLY A:224 , ASP A:225 , THR A:228 , LYS A:231 , GLY A:248 , CYS A:280 , GLN A:327 , ARG A:330 , GLU A:378 , PHE A:380BINDING SITE FOR RESIDUE NAD A 500
2AC2SOFTWAREASN A:65 , LYS A:69 , ASP A:72 , HOH A:749 , GLU D:75 , ARG D:109BINDING SITE FOR RESIDUE GOL A 501
3AC3SOFTWAREILE A:139 , GLN B:426 , HOH B:682BINDING SITE FOR RESIDUE GOL B 501
4AC4SOFTWAREILE B:145 , ALA B:146 , PRO B:147 , TRP B:148 , LYS B:172 , SER B:174 , GLU B:175 , GLY B:204 , GLY B:208 , ASN B:209 , ILE B:222 , THR B:223 , GLY B:224 , ASP B:225 , THR B:228 , LYS B:231 , LEU B:247 , GLY B:248 , CYS B:280 , GLN B:327 , GLU B:378 , PHE B:380BINDING SITE FOR RESIDUE NAD B 502
5AC5SOFTWAREASN B:65 , LYS B:69 , HOH B:672BINDING SITE FOR RESIDUE GOL B 503
6AC6SOFTWAREILE C:145 , ALA C:146 , PRO C:147 , TRP C:148 , LYS C:172 , SER C:174 , GLU C:175 , GLY C:204 , GLY C:208 , ASN C:209 , ILE C:212 , ILE C:222 , THR C:223 , GLY C:224 , ASP C:225 , THR C:228 , LYS C:231 , CYS C:280 , GLN C:327 , ARG C:330 , GLU C:378 , PHE C:380BINDING SITE FOR RESIDUE NAD C 500
7AC7SOFTWAREARG B:109 , ASN C:65 , LYS C:69BINDING SITE FOR RESIDUE GOL C 501
8AC8SOFTWAREILE D:145 , ALA D:146 , PRO D:147 , TRP D:148 , ASN D:149 , LYS D:172 , SER D:174 , GLU D:175 , GLY D:204 , GLU D:205 , GLY D:208 , ASN D:209 , ILE D:212 , ILE D:222 , THR D:223 , GLY D:224 , ASP D:225 , THR D:228 , LYS D:231 , GLY D:248 , CYS D:280 , GLN D:327 , ARG D:330 , GLU D:378 , PHE D:380 , HOH D:675BINDING SITE FOR RESIDUE NAD D 500
9AC9SOFTWAREARG A:109 , ASN D:65 , LEU D:68 , LYS D:69 , ASP D:72BINDING SITE FOR RESIDUE GOL D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F3X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F3X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F3X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F3X)

(-) Exons   (0, 0)

(no "Exon" information available for 4F3X)

(-) 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:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4f3xa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eee......hhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhhh...eeee..............eeee.....hhhhhh.....eeeeeee....hhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhhheeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3x A   0 mmDTQLLIGSRFEAGTEAEEHILNPRTGAGIIDLAEASHAQIDAAVDAAERAFVGWSQTTPAERSNALLKIADAIEKEADEFAALEALNCGKPINAVKNDELPAIIDCWRFFAGAVRNLHAPAAGEYLPGHTSmIRRDPIGIVGSIAPWNYPLmmmAWKLAPAIGGGNTVVFKPSEQTPLTALKLARLIADILPEGVVNVITGRGETVGNALINHPKVGmVSITGDIATGKKVLAAAAKTVKRTHLELGGKAPVIVYGDADLEAVVNGIRTFGYYNAGQDCTAACRIYAEAGIYEKLVADLTSAVSTIRYNLDDDTENEIGPLISRRQRDRVASFVERAADQKHIEITTGGRTGSDEGFFFQPTVVAGATQEDEIVRREVFGPVVSVTRFTGKDDAVAWANDSDYGLASSVWTKDISKAmRAASRLQYGCTWINTHFmLTNEmPHGGIKQSGYGKDmSVYALEDYTAVRHImINHG 475
                            ||       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 |    
                            ||                                                                                                                                 133-MSE             153-MSE                                                           219-MSE                                                                                                                                                                                                 419-MSE           437-MSE|           456-MSE        471-MSE
                            0-MSE                                                                                                                                                   154-MSE                                                                                                                                                                                                                                                                                         442-MSE                             
                             1-MSE                                                                                                                                                   155-MSE                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4f3xb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhh....eeee..............eeee.....hhhhhh.....eeeeeee....hhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhhheeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3x B   0 mmDTQLLIGSRFEAGTEAEEHILNPRTGAGIIDLAEASHAQIDAAVDAAERAFVGWSQTTPAERSNALLKIADAIEKEADEFAALEALNCGKPINAVKNDELPAIIDCWRFFAGAVRNLHAPAAGEYLPGHTSmIRRDPIGIVGSIAPWNYPLmmmAWKLAPAIGGGNTVVFKPSEQTPLTALKLARLIADILPEGVVNVITGRGETVGNALINHPKVGmVSITGDIATGKKVLAAAAKTVKRTHLELGGKAPVIVYGDADLEAVVNGIRTFGYYNAGQDCTAACRIYAEAGIYEKLVADLTSAVSTIRYNLDDDTENEIGPLISRRQRDRVASFVERAADQKHIEITTGGRTGSDEGFFFQPTVVAGATQEDEIVRREVFGPVVSVTRFTGKDDAVAWANDSDYGLASSVWTKDISKAmRAASRLQYGCTWINTHFmLTNEmPHGGIKQSGYGKDmSVYALEDYTAVRHImINHG 475
                            ||       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 |    
                            ||                                                                                                                                 133-MSE             153-MSE                                                           219-MSE                                                                                                                                                                                                 419-MSE           437-MSE|           456-MSE        471-MSE
                            0-MSE                                                                                                                                                   154-MSE                                                                                                                                                                                                                                                                                         442-MSE                             
                             1-MSE                                                                                                                                                   155-MSE                                                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4f3xc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eee......hhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhhhhhhhhhhh...eeee..............eeee.....hhhhhh.....eeeeeee....hhhhhhhh.......eee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhhheeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3x C   0 mmDTQLLIGSRFEAGTEAEEHILNPRTGAGIIDLAEASHAQIDAAVDAAERAFVGWSQTTPAERSNALLKIADAIEKEADEFAALEALNCGKPINAVKNDELPAIIDCWRFFAGAVRNLHAPAAGEYLPGHTSmIRRDPIGIVGSIAPWNYPLmmmAWKLAPAIGGGNTVVFKPSEQTPLTALKLARLIADILPEGVVNVITGRGETVGNALINHPKVGmVSITGDIATGKKVLAAAAKTVKRTHLELGGKAPVIVYGDADLEAVVNGIRTFGYYNAGQDCTAACRIYAEAGIYEKLVADLTSAVSTIRYNLDDDTENEIGPLISRRQRDRVASFVERAADQKHIEITTGGRTGSDEGFFFQPTVVAGATQEDEIVRREVFGPVVSVTRFTGKDDAVAWANDSDYGLASSVWTKDISKAmRAASRLQYGCTWINTHFmLTNEmPHGGIKQSGYGKDmSVYALEDYTAVRHImINHG 475
                            ||       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 |    
                            ||                                                                                                                                 133-MSE             153-MSE                                                           219-MSE                                                                                                                                                                                                 419-MSE           437-MSE|           456-MSE        471-MSE
                            0-MSE                                                                                                                                                   154-MSE                                                                                                                                                                                                                                                                                         442-MSE                             
                             1-MSE                                                                                                                                                   155-MSE                                                                                                                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4f3xd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhh.......eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.....eeee..............eeee.....hhhhhh.....eeeeeee....hhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhhheeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3x D   1 mDTQLLIGSRFEAGTEAEEHILNPRTGAGIIDLAEASHAQIDAAVDAAERAFVGWSQTTPAERSNALLKIADAIEKEADEFAALEALNCGKPINAVKNDELPAIIDCWRFFAGAVRNLHAPAAGEYLPGHTSmIRRDPIGIVGSIAPWNYPLmmmAWKLAPAIGGGNTVVFKPSEQTPLTALKLARLIADILPEGVVNVITGRGETVGNALINHPKVGmVSITGDIATGKKVLAAAAKTVKRTHLELGGKAPVIVYGDADLEAVVNGIRTFGYYNAGQDCTAACRIYAEAGIYEKLVADLTSAVSTIRYNLDDDTENEIGPLISRRQRDRVASFVERAADQKHIEITTGGRTGSDEGFFFQPTVVAGATQEDEIVRREVFGPVVSVTRFTGKDDAVAWANDSDYGLASSVWTKDISKAmRAASRLQYGCTWINTHFmLTNEmPHGGIKQSGYGKDmSVYALEDYTAVRHImINHG 475
                            |       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|    
                            |                                                                                                                                 133-MSE             153-MSE                                                           219-MSE                                                                                                                                                                                                 419-MSE           437-MSE|           456-MSE        471-MSE
                            1-MSE                                                                                                                                                  154-MSE                                                                                                                                                                                                                                                                                         442-MSE                             
                                                                                                                                                                                    155-MSE
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F3X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F3X)

(-) Gene Ontology  (5, 5)

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(-) Related Entries Specified in the PDB File

4dal APOENZYME RELATED ID: NYSGRC-012061 RELATED DB: TARGETTRACK