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(-) Description

Title :  THERMOSTABLE PHOSPHITE DEHYDROGENASE IN COMPLEX WITH NAD AND SULFITE
 
Authors :  Y. Zou, H. Zhang, S. K. Nair
Date :  14 Mar 12  (Deposition) - 30 May 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B (1x),C (1x)
Keywords :  D2-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 - PHOSPHITE DEHYDROGENASE (THERMOSTABLE VARIANT)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PSEUDOMONAS STUTZERI
    Organism Taxid: 316

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  B (1x)C (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO34Ligand/IonSULFITE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO32Ligand/IonSULFITE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO31Ligand/IonSULFITE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:76 , GLY A:77 , THR A:104 , GLY A:152 , GLY A:154 , ALA A:155 , ILE A:156 , HIS A:174 , GLU A:175 , ALA A:176 , ALA A:207 , LEU A:208 , PRO A:209 , PRO A:235 , CYS A:236 , ARG A:237 , ASP A:261 , HIS A:292 , GLY A:294 , SO3 A:402 , HOH A:501 , HOH A:509 , HOH A:514 , HOH A:560 , HOH A:578 , HOH A:611 , HOH A:637BINDING SITE FOR RESIDUE NAD A 401
2AC2SOFTWAREMET A:53 , LEU A:75 , LYS A:76 , GLY A:77 , LEU A:100 , ARG A:237 , HIS A:292 , NAD A:401 , HOH A:637BINDING SITE FOR RESIDUE SO3 A 402
3AC3SOFTWARELYS B:76 , GLY B:77 , THR B:104 , GLY B:152 , GLY B:154 , ALA B:155 , ILE B:156 , HIS B:174 , GLU 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 , VAL B:262 , HIS B:292 , GLY B:294 , SO3 B:402 , HOH B:504 , HOH B:528 , HOH B:537 , HOH B:559 , HOH B:574 , HOH B:600 , HOH B:624 , HOH B:647 , HOH B:668 , HOH B:676BINDING SITE FOR RESIDUE NAD B 401
4AC4SOFTWAREMET B:53 , LEU B:75 , LYS B:76 , GLY B:77 , ARG B:237 , HIS B:292 , NAD B:401BINDING SITE FOR RESIDUE SO3 B 402
5AC5SOFTWARELYS C:76 , GLY C:77 , THR C:104 , GLY C:152 , GLY C:154 , ALA C:155 , ILE C:156 , HIS C:174 , GLU C:175 , ALA C:176 , ALA C:207 , LEU C:208 , PRO C:209 , LEU C:217 , PRO C:235 , CYS C:236 , ARG C:237 , ASP C:261 , HIS C:292 , GLY C:294 , SO3 C:402 , HOH C:515 , HOH C:524 , HOH C:534 , HOH C:552 , HOH C:578BINDING SITE FOR RESIDUE NAD C 401
6AC6SOFTWAREMET C:53 , LEU C:75 , LYS C:76 , GLY C:77 , ARG C:237 , HIS C:292 , NAD C:401BINDING SITE FOR RESIDUE SO3 C 402
7AC7SOFTWAREMET D:53 , LEU D:75 , LYS D:76 , GLY D:77 , LEU D:100 , ARG D:237 , HIS D:292BINDING SITE FOR RESIDUE SO3 D 401
8AC8SOFTWARELYS D:76 , THR D:104 , GLY D:152 , GLY D:154 , ALA D:155 , ILE D:156 , HIS D:174 , GLU D:175 , ALA D:176 , ALA D:207 , LEU D:208 , PRO D:209 , LEU D:217 , PRO D:235 , CYS D:236 , ARG D:237 , ASP D:261 , HIS D:292 , GLY D:294 , HOH D:524 , HOH D:532BINDING SITE FOR RESIDUE NAD D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E5K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E5K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E5K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E5K)

(-) Exons   (0, 0)

(no "Exon" information available for 4E5K)

(-) 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:329
 aligned with PTXD_PSEST | O69054 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:329
                                    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         
           PTXD_PSEST     1 MLPKLVITHRVHDEILQLLAPHCELMTNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGEFQGWQPQFYGTGLDNATVGILGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNIIQVLAGARPINAANRLP 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..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5k A   1 MLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGKFRGWQPRFYGTGLDNATVGFLGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLP 329
                                    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         


Chain B from PDB  Type:PROTEIN  Length:329
 aligned with PTXD_PSEST | O69054 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:329
                                    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         
           PTXD_PSEST     1 MLPKLVITHRVHDEILQLLAPHCELMTNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGEFQGWQPQFYGTGLDNATVGILGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNIIQVLAGARPINAANRLP 329
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhh...eee........hhhhhhhhhh...eeee......hhhhhhh.....eeee........hhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhheee.hhhhhhhhh.eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee..hhhhh..........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5k B   1 MLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGKFRGWQPRFYGTGLDNATVGFLGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLP 329
                                    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         


Chain C from PDB  Type:PROTEIN  Length:328
 aligned with PTXD_PSEST | O69054 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:329
                                    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         
           PTXD_PSEST     1 MLPKLVITHRVHDEILQLLAPHCELMTNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGEFQGWQPQFYGTGLDNATVGILGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNIIQVLAGARPINAANRLP 329
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhh...eee........hhhhhhhhh....eeee......hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....-.............eeeee..hhhhhhhhhhh.....eeeee.....hhhhhhhhheee.hhhhhhh...eeee............hhhhhhh....eeeee..hhhhhhhhhhhhhhhhh.eeeeee..hhhhh..........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5k C   1 MLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGKFR-WQPRFYGTGLDNATVGFLGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLP 329
                                    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         
                                                                                                                                                             132 |                                                                                                                                                                                                   
                                                                                                                                                               134                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:329
 aligned with PTXD_PSEST | O69054 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:329
                                    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         
           PTXD_PSEST     1 MLPKLVITHRVHDEILQLLAPHCELMTNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGEFQGWQPQFYGTGLDNATVGILGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNIIQVLAGARPINAANRLP 329
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhh...eee........hhhhhhhhhh...eeee......hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhh.ee.hhhhhhhhh.eeee............hhhhhh......eeee..hhhhhhhhhhhhhhhh....eeee..hhhhh..........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5k D   1 MLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAMMAFMPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRAADAFVRSGKFRGWQPRFYGTGLDNATVGFLGMGAIGLAMADRLQGWGATLQYHEAKALDTQTEQRLGLRQVACSELFASSDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAVRLEIERCAAQNILQALAGERPINAVNRLP 329
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4E5K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E5K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E5K)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PTXD_PSEST | O69054)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0050609    phosphonate dehydrogenase activity    Catalysis of the reaction: H(2)O + NAD(+) + phosphonate = 2 H(+) + NADH + phosphate.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTXD_PSEST | O69054: 4e5m 4e5n 4e5p 4ebf 4nu5 4nu6

(-) Related Entries Specified in the PDB File

4e5m 4e5n 4e5p