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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAMERIC PYRIDOXAL 4-DEHYDROGENASE FROM MESORHIZOBIUM LOTI
 
Authors :  H. N. Chu
Date :  08 Jun 10  (Deposition) - 08 Jun 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pyridoxal, Tpldh, 4-Pyridoxolactone, Short Chain Dehydrogenase/Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. N. Chu, J. Kobayashi, Y. Yoshikane, B. Mikami, T. Yagi
Crystal Structure Of Tetrameric Pyridoxal 4-Dehydrogenase From Mesorhizobium Loti
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
    ChainsA, B, C, D
    EC Number1.1.1.107
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMLR6807, PLDH-T
    Organism ScientificMESORHIZOBIUM LOTI
    Organism Taxid381
    SynonymPYRIDOXAL 4-DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , GLN A:17 , GLY A:18 , ILE A:19 , ASP A:38 , ILE A:39 , ALA A:60 , ASP A:61 , ILE A:62 , ASN A:88 , ALA A:89 , SER A:90 , VAL A:111 , ILE A:139 , ALA A:140 , SER A:141 , TYR A:154 , LYS A:158 , PRO A:184 , GLY A:185 , LEU A:186 , ILE A:187 , SER A:189 , GLY A:191 , VAL A:192 , HOH A:301 , HOH A:357BINDING SITE FOR RESIDUE NAD A 251
2AC2SOFTWAREGLY B:14 , GLN B:17 , GLY B:18 , ILE B:19 , ASP B:38 , ILE B:39 , ALA B:60 , ASP B:61 , ILE B:62 , ASN B:88 , ALA B:89 , SER B:90 , ILE B:139 , ALA B:140 , SER B:141 , TYR B:154 , LYS B:158 , PRO B:184 , GLY B:185 , LEU B:186 , ILE B:187 , SER B:189 , GLY B:191 , VAL B:192 , HOH B:312 , HOH B:347BINDING SITE FOR RESIDUE NAD B 251
3AC3SOFTWAREGLY C:14 , GLN C:17 , GLY C:18 , ILE C:19 , ASP C:38 , ILE C:39 , ALA C:60 , ASP C:61 , ILE C:62 , ASN C:88 , ALA C:89 , SER C:90 , VAL C:92 , ILE C:139 , ALA C:140 , SER C:141 , TYR C:154 , LYS C:158 , PRO C:184 , GLY C:185 , LEU C:186 , ILE C:187 , SER C:189 , GLY C:191 , VAL C:192BINDING SITE FOR RESIDUE NAD C 251
4AC4SOFTWAREGLY D:14 , GLN D:17 , GLY D:18 , ILE D:19 , ASP D:38 , ILE D:39 , ALA D:60 , ASP D:61 , ILE D:62 , ASN D:88 , ALA D:89 , SER D:90 , ILE D:139 , ALA D:140 , SER D:141 , TYR D:154 , LYS D:158 , PRO D:184 , GLY D:185 , LEU D:186 , ILE D:187 , SER D:189 , GLY D:191 , VAL D:192 , HOH D:350BINDING SITE FOR RESIDUE NAD D 251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NDR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NDR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NDR)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.PLDH_RHILO141-169
 
 
 
  4A:141-169
B:141-169
C:141-169
D:141-169

(-) Exons   (0, 0)

(no "Exon" information available for 3NDR)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:247
 aligned with PLDH_RHILO | Q988B7 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           PLDH_RHILO     2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQMRAAGKAGRVISIASNTFFAGTPNMAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEMLQAMKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGMVRH 248
               SCOP domains d3ndra_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:141-169    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndr A   2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQmRAAGKAGRVISIASNTFFAGTPNmAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEmLQAmKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGmVRH 248
                                    11        21        31        41        51        61        71        81        91       101       111       121     | 131       141       151       161       171       181       191       201    |  211       221       231       241   |   
                                                                                                                                                       127-MSE                 151-MSE                                                206-MSE                                245-MSE
                                                                                                                                                                                                                                          210-MSE                                  

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with PLDH_RHILO | Q988B7 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           PLDH_RHILO     2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQMRAAGKAGRVISIASNTFFAGTPNMAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEMLQAMKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGMVRH 248
               SCOP domains d3ndrb_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:141-169    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndr B   2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQmRAAGKAGRVISIASNTFFAGTPNmAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEmLQAmKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGmVRH 248
                                    11        21        31        41        51        61        71        81        91       101       111       121     | 131       141       151       161       171       181       191       201    |  211       221       231       241   |   
                                                                                                                                                       127-MSE                 151-MSE                                                206-MSE                                245-MSE
                                                                                                                                                                                                                                          210-MSE                                  

Chain C from PDB  Type:PROTEIN  Length:247
 aligned with PLDH_RHILO | Q988B7 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           PLDH_RHILO     2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQMRAAGKAGRVISIASNTFFAGTPNMAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEMLQAMKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGMVRH 248
               SCOP domains d3ndrc_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:141-169    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndr C   2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQmRAAGKAGRVISIASNTFFAGTPNmAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEmLQAmKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGmVRH 248
                                    11        21        31        41        51        61        71        81        91       101       111       121     | 131       141       151       161       171       181       191       201    |  211       221       231       241   |   
                                                                                                                                                       127-MSE                 151-MSE                                                206-MSE                                245-MSE
                                                                                                                                                                                                                                          210-MSE                                  

Chain D from PDB  Type:PROTEIN  Length:247
 aligned with PLDH_RHILO | Q988B7 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           PLDH_RHILO     2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQMRAAGKAGRVISIASNTFFAGTPNMAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEMLQAMKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGMVRH 248
               SCOP domains d3ndrd_ D: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------adh_short-3ndrD01 D:8-173                                                                                                                                             --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------adh_short-3ndrD02 D:8-173                                                                                                                                             --------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------adh_short-3ndrD03 D:8-173                                                                                                                                             --------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------adh_short-3ndrD04 D:8-173                                                                                                                                             --------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:141-169    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndr D   2 TERLAGKTALVTGAAQGIGKAIAARLAADGATVIVSDINAEGAKAAAASIGKKARAIAADISDPGSVKALFAEIQALTGGIDILVNNASIVPFVAWDDVDLDHWRKIIDVNLTGTFIVTRAGTDQmRAAGKAGRVISIASNTFFAGTPNmAAYVAAKGGVIGFTRALATELGKYNITANAVTPGLIESDGVKASPHNEAFGFVEmLQAmKGKGQPEHIADVVSFLASDDARWITGQTLNVDAGmVRH 248
                                    11        21        31        41        51        61        71        81        91       101       111       121     | 131       141       151       161       171       181       191       201    |  211       221       231       241   |   
                                                                                                                                                       127-MSE                 151-MSE                                                206-MSE                                245-MSE
                                                                                                                                                                                                                                          210-MSE                                  

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NDR)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PLDH_RHILO | Q988B7)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0050235    pyridoxal 4-dehydrogenase activity    Catalysis of the reaction: NAD(+) + pyridoxal = 4-pyridoxolactone + H(+) + NADH.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0042820    vitamin B6 catabolic process    The chemical reactions and pathways resulting in the breakdown of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.

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 Related Entries

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UniProtKB/Swiss-Prot
        PLDH_RHILO | Q988B73nug 3rwb

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