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(-) Description

Title :  SEMET THERMOSTABLE PHOSPHITE DEHYDROGENASE GLU175-ALA MUTANT
 
Authors :  Y. Zou, H. Zhang, S. K. Nair
Date :  23 Mar 12  (Deposition) - 30 May 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  D-2-Hydroxyacid Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zou, H. Zhang, J. S. Brunzelle, T. W. Johannes, R. Woodyer, J. E. Hung N. Nair, W. A. Van Der Donk, H. Zhao, S. K. Nair
Crystal Structures Of Phosphite Dehydrogenase Provide Insights Into Nicotinamide Cofactor Regeneration.
Biochemistry V. 51 4263 2012
PubMed-ID: 22564171  |  Reference-DOI: 10.1021/BI2016926

(-) Compounds

Molecule 1 - THERMOSTABLE PHOSPHITE DEHYDROGENASE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PTX
    Mutation: YES
    Organism Scientific: PSEUDOMONAS STUTZERI
    Organism Taxid: 316

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A    F
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   CD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 42)

Asymmetric Unit (2, 42)
No.NameCountTypeFull Name
1MSE38Mod. Amino AcidSELENOMETHIONINE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (2, 15)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:76 , THR A:104 , MSE A:153 , GLY A:154 , ALA A:155 , ILE A:156 , ALA A:175 , ALA A:176 , LYS A:177 , LEU A:208 , PRO A:209 , PRO A:235 , CYS A:236 , ARG A:237 , ASP A:261 , HIS A:292 , GLY A:294 , HOH A:902 , HOH A:909 , HOH A:920 , HOH A:958 , HOH A:969BINDING SITE FOR RESIDUE NAD A 800
2AC2SOFTWARELYS B:76 , GLY B:77 , THR B:104 , MSE B:153 , GLY B:154 , ALA B:155 , ILE B:156 , ALA B:175 , ALA B:176 , ALA B:207 , LEU B:208 , PRO B:209 , PRO B:235 , CYS B:236 , ARG B:237 , ASP B:261 , HIS B:292 , GLY B:294 , HOH B:902 , HOH B:913 , HOH B:932 , HOH B:936 , HOH B:977 , HOH B:1016 , HOH B:1019BINDING SITE FOR RESIDUE NAD B 800
3AC3SOFTWARETHR C:104 , GLY C:152 , MSE C:153 , GLY C:154 , ALA C:155 , ILE C:156 , ALA C:175 , ALA C:176 , ALA C:207 , LEU C:208 , PRO C:209 , THR C:214 , PRO C:235 , CYS C:236 , ASP C:261 , HIS C:292 , GLY C:294 , HOH C:913 , HOH C:934 , HOH C:940 , HOH C:967 , HOH C:998BINDING SITE FOR RESIDUE NAD C 800
4AC4SOFTWARELYS D:76 , GLY D:77 , THR D:104 , MSE D:153 , GLY D:154 , ALA D:155 , ILE D:156 , ALA D:176 , LEU D:208 , PRO D:209 , PRO D:235 , CYS D:236 , ARG D:237 , ASP D:261 , VAL D:262 , HIS D:292 , GLY D:294 , HOH D:903 , HOH D:921 , HOH D:986BINDING SITE FOR RESIDUE NAD D 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EBF)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhh...eee........hhhhhhhhhh...eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeee..hhhhhhhhhhh.....eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhhh....eeeee..hhhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ebf A   2 LPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAmmAFmPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGFLGmGAIGLAmADRLQGWGATLQYHAAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEmEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLPKANP 333
                                    11        21        31        41       |51 |      61        71        81        91       101       111       121       131       141       151 |     161       171       181       191       201       211       221       231       241       251       261   |   271       281       291       301       311       321       331  
                                                                          49-MSE                                                                                                 153-MSE  |                                                                                                      265-MSE                                                                
                                                                           50-MSE                                                                                                       160-MSE                                                                                                                                                                         
                                                                              53-MSE                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhh...eee........hhhhhhhhhh...eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh......eeee..hhhhhhhhhhhhhhhh....eeee..hhhhh..........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ebf B   1 mLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAmmAFmPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGFLGmGAIGLAmADRLQGWGATLQYHAAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEmEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLPK 330
                            |       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
                            1-MSE                                          49-MSE                                                                                                 153-MSE  |                                                                                                      265-MSE                                                             
                                                                            50-MSE                                                                                                       160-MSE                                                                                                                                                                      
                                                                               53-MSE                                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhh...eee........hhhhhhhhhh...eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeeee..hhhhhhhhhhh.....eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ebf C   0 GmLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAmmAFmPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGFLGmGAIGLAmADRLQGWGATLQYHAAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEmEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRL 328
                             |       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         
                             1-MSE                                          49-MSE                                                                                                 153-MSE  |                                                                                                      265-MSE                                                           
                                                                             50-MSE                                                                                                       160-MSE                                                                                                                                                                    
                                                                                53-MSE                                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhh...eee........hhhhhhhhhh...eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ebf D   2 LPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAmmAFmPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGFLGmGAIGLAmADRLQGWGATLQYHAAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEmEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLPKA 331
                                    11        21        31        41       |51 |      61        71        81        91       101       111       121       131       141       151 |     161       171       181       191       201       211       221       231       241       251       261   |   271       281       291       301       311       321       331
                                                                          49-MSE                                                                                                 153-MSE  |                                                                                                      265-MSE                                                              
                                                                           50-MSE                                                                                                       160-MSE                                                                                                                                                                       
                                                                              53-MSE                                                                                                                                                                                                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhh...eeee.......hhhhhhhhhh...eeee......hhhhhhh.....eeee...hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeeee..hhhhhhhhhhh.....eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh......eeee..hhhhhhhhhhhhhhhh....eeee..hhhhh..........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ebf E   2 LPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAmmAFmPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGFLGmGAIGLAmADRLQGWGATLQYHAAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEmEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPI 322
                                    11        21        31        41       |51 |      61        71        81        91       101       111       121       131       141       151 |     161       171       181       191       201       211       221       231       241       251       261   |   271       281       291       301       311       321 
                                                                          49-MSE                                                                                                 153-MSE  |                                                                                                      265-MSE                                                     
                                                                           50-MSE                                                                                                       160-MSE                                                                                                                                                              
                                                                              53-MSE                                                                                                                                                                                                                                                                         


Chain F from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhheee........hhhhhhhhh....eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeee..hhhhhhhhhhh.....eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ebf F   2 LPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAmmAFmPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGFLGmGAIGLAmADRLQGWGATLQYHAAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEmEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNR 327
                                    11        21        31        41       |51 |      61        71        81        91       101       111       121       131       141       151 |     161       171       181       191       201       211       221       231       241       251       261   |   271       281       291       301       311       321      
                                                                          49-MSE                                                                                                 153-MSE  |                                                                                                      265-MSE                                                          
                                                                           50-MSE                                                                                                       160-MSE                                                                                                                                                                   
                                                                              53-MSE
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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 Related Entries

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

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        PTXD_PSEST | O69054: 4e5k 4e5m 4e5n 4e5p 4nu5 4nu6

(-) Related Entries Specified in the PDB File

4e5k 4e5m 4e5n 4e5p