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(-) Description

Title :  PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND BETA-PHENYLPROPIONATE
 
Authors :  J. L. Vanhooke, J. B. Thoden, N. M. W. Brunhuber, J. L. Blanchard, H. M. Holden
Date :  02 Oct 98  (Deposition) - 18 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amino Acid Dehydrogenase, Oxidative Deamination Mechanism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Vanhooke, J. B. Thoden, N. M. Brunhuber, J. S. Blanchard, H. M. Holden
Phenylalanine Dehydrogenase From Rhodococcus Sp. M4: High-Resolution X-Ray Analyses Of Inhibitory Ternary Complexes Reveal Key Features In The Oxidative Deamination Mechanism.
Biochemistry V. 38 2326 1999
PubMed-ID: 10029526  |  Reference-DOI: 10.1021/BI982244Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHENYLALANINE DEHYDROGENASE
    Cell Line: BL21
    Chains: A
    EC Number: 1.4.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBL-1B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: RHODOCOCCUS SP.
    Organism Taxid: 1831
 
Molecule 2 - PHENYLALANINE DEHYDROGENASE
    Cell Line: BL21
    Chains: B
    EC Number: 1.4.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBL-1B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: RHODOCOCCUS SP.
    Organism Taxid: 1831

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1HCI2Ligand/IonHYDROCINNAMIC ACID
2K1Ligand/IonPOTASSIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:111 , HOH B:151 , LEU B:570 , SER B:572 , ASP B:574 , LEU B:576 , PO4 B:900BINDING SITE FOR RESIDUE K B 850
2AC2SOFTWARESER B:401 , SER B:404 , LYS B:458 , LEU B:570 , K B:850BINDING SITE FOR RESIDUE PO4 B 900
3AC3SOFTWARESER A:149 , THR A:153 , GLY A:182 , GLY A:184 , ALA A:185 , VAL A:186 , ASP A:205 , THR A:206 , CYS A:238 , ALA A:239 , MET A:240 , ALA A:260 , ALA A:261 , ASN A:288 , HCI A:361 , HOH A:401 , HOH A:426BINDING SITE FOR RESIDUE NAD A 360
4AC4SOFTWAREGLY A:39 , GLY A:40 , LYS A:66 , LYS A:78 , GLY A:116 , ASN A:262 , NAD A:360BINDING SITE FOR RESIDUE HCI A 361
5AC5SOFTWAREHOH B:4 , HOH B:36 , ARG B:442 , SER B:549 , THR B:553 , GLY B:582 , LEU B:583 , GLY B:584 , ALA B:585 , VAL B:586 , ALA B:604 , ASP B:605 , THR B:606 , ARG B:610 , LEU B:624 , CYS B:638 , ALA B:639 , ALA B:660 , ALA B:661 , ASN B:662 , ASN B:688 , HCI B:761BINDING SITE FOR RESIDUE NAD B 760
6AC6SOFTWAREHOH B:27 , HOH B:36 , GLY B:439 , GLY B:440 , LYS B:466 , LYS B:478 , GLY B:516 , ASN B:662 , NAD B:760BINDING SITE FOR RESIDUE HCI B 761

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BXG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BXG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BXG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BXG)

(-) Exons   (0, 0)

(no "Exon" information available for 1BXG)

(-) 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:349
 aligned with DHPH_RHOSO | Q59771 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:349
                                    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       341         
           DHPH_RHOSO     2 SIDSALNWDGEMTVTRFDRETGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREAS 350
               SCOP domains d1bxga2 A:1-148 Phenylalanine dehydrogenase                                                                                                         d1bxga1 A:149-349 Phenylalanine dehydrogenase                                                                                                                                                             SCOP domains
               CATH domains --1bxgA01 A:3-64,A:75-136,A:339-349                             ----------1bxgA01 A:3-64,A:75-136,A:339-349                             1bxgA02 A:137-338 NAD(P)-binding Rossmann-like Domain                                                                                                                                                     1bxgA01     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh......eeeeeee....eeeeeeeee.....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeee...hhh..hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh..eeeee...hhhhhhhhhh......hhhhhh....eeee........hhhhhh................hhhhhhhhhh......hhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bxg A   1 SIDSALNWDGEMTVTRFDSKTGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREAS 349
                                    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         


Chain B from PDB  Type:PROTEIN  Length:347
 aligned with DHPH_RHOSO | Q59771 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:347
                                    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       341       
           DHPH_RHOSO     2 SIDSALNWDGEMTVTRFDRETGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRARE 348
               SCOP domains d1bxgb2 B:401-548 Phenylalanine dehydrogenase                                                                                                       d1bxgb1 B:549-747 Phenylalanine dehydrogenase                                                                                                                                                           SCOP domains
               CATH domains ----1bxgB01 B:405-464,B:475-536,B:739-747                       ----------1bxgB01 B:405-464,B:475-536,B:739-747                         1bxgB02 B:537-738 NAD(P)-binding Rossmann-like Domain                                                                                                                                                     1bxgB01   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....eeeeeee....eeeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh.........hhh......hhhhhhhhhhhhhhhhhhh........eeeee.....hhhhhhhhhh...eeeee...hhhhhhhhh.................eeee........hhhh..................hhhhhhhhh.......hhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bxg B 401 SIDSALNWDGEMTVTRFDRMTGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRARE 747
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740
   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  (2, 4)

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

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BXG)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DHPH_RHOSO | Q59771)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0016639    oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0050175    phenylalanine dehydrogenase activity    Catalysis of the reaction: L-phenylalanine + H2O + NAD+ = phenylpyruvate + NH3 + NADH.
biological process
    GO:0009094    L-phenylalanine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
    GO:0006559    L-phenylalanine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    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
        DHPH_RHOSO | Q59771: 1bw9 1c1d 1c1x

(-) Related Entries Specified in the PDB File

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