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(-) Description

Title :  L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND L-3-PHENYLLACTATE
 
Authors :  J. L. Vanhooke, J. B. Thoden
Date :  22 Jul 99  (Deposition) - 30 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amino Acid Dehydrogenase, Oxidative Deamination Mechanism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Brunhuber, J. B. Thoden, J. S. Blanchard, J. L. Vanhooke
Rhodococcus L-Phenylalanine Dehydrogenase: Kinetics, Mechanism, And Structural Basis For Catalytic Specificity.
Biochemistry V. 39 9174 2000
PubMed-ID: 10924111  |  Reference-DOI: 10.1021/BI000494C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-PHENYLALANINE DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBL-1B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PLASMID
    Organism Scientific: RHODOCOCCUS SP.
    Organism Taxid: 1831
 
Molecule 2 - PROTEIN (L-PHENYLALANINE DEHYDROGENASE)
    Chains: B
    Engineered: YES
    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  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1HFA2Ligand/IonALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID
2IPA3Ligand/IonISOPROPYL ALCOHOL
3K4Ligand/IonPOTASSIUM ION
4NA1Ligand/IonSODIUM ION
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6PO41Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:118 , THR A:121 , HOH A:1488 , HOH A:1574BINDING SITE FOR RESIDUE K A 850
02AC2SOFTWARELEU B:170 , SER B:172 , ASP B:174 , LEU B:176 , PO4 B:880 , HOH B:1187 , HOH B:1408BINDING SITE FOR RESIDUE K B 851
03AC3SOFTWAREASP B:118 , THR B:121 , HOH B:1511 , HOH B:1645 , HOH B:1762BINDING SITE FOR RESIDUE K B 852
04AC4SOFTWARETRP A:8 , GLY A:10 , HOH A:1868 , ARG B:16 , PHE B:17BINDING SITE FOR RESIDUE K A 853
05AC5SOFTWAREARG A:87 , TRP A:95 , ASN A:120 , ASN A:122 , ASP A:125BINDING SITE FOR RESIDUE NA A 855
06AC6SOFTWARESER B:1 , SER B:4 , THR B:54 , LYS B:58 , LEU B:170 , LEU B:176 , K B:851 , HOH B:1040 , HOH B:1175 , HOH B:1408 , HOH B:1419 , HOH B:1608BINDING SITE FOR RESIDUE PO4 B 880
07AC7SOFTWAREGLY A:39 , GLY A:40 , MET A:63 , LYS A:66 , LYS A:78 , PRO A:117 , PHE A:137 , ALA A:292 , NAD A:360 , HOH A:1021 , HOH A:1171BINDING SITE FOR RESIDUE HFA A 361
08AC8SOFTWAREASP A:118 , SER A:149 , THR A:153 , GLY A:182 , LEU A:183 , GLY A:184 , ALA A:185 , VAL A:186 , ASP A:205 , THR A:206 , ARG A:210 , LEU A:224 , CYS A:238 , ALA A:239 , MET A:240 , ALA A:260 , ALA A:261 , ASN A:262 , ASN A:288 , HFA A:361 , HOH A:1079 , HOH A:1171 , HOH A:1284 , HOH A:1311 , HOH A:1488 , HOH A:1582 , HOH A:1588 , HOH A:1600 , HOH A:1746 , HOH A:1813BINDING SITE FOR RESIDUE NAD A 360
09AC9SOFTWARESER B:149 , THR B:153 , GLY B:182 , GLY B:184 , ALA B:185 , VAL B:186 , ASP B:205 , THR B:206 , ARG B:210 , CYS B:238 , ALA B:239 , MET B:240 , ALA B:260 , ALA B:261 , ASN B:262 , ASN B:288 , HFA B:761 , HOH B:1027 , HOH B:1173 , HOH B:1274 , HOH B:1511 , HOH B:1618BINDING SITE FOR RESIDUE NAD B 760
10BC1SOFTWAREGLY B:39 , GLY B:40 , MET B:63 , LYS B:66 , LYS B:78 , GLY B:116 , PRO B:117 , PHE B:137 , LEU B:295 , NAD B:760 , HOH B:1173 , HOH B:1890BINDING SITE FOR RESIDUE HFA B 761
11BC2SOFTWAREALA A:276 , HOH A:1294 , LEU B:34 , GLY B:35 , PRO B:73BINDING SITE FOR RESIDUE IPA B 860
12BC3SOFTWARETHR A:15 , LEU A:49 , LEU B:6 , THR B:13 , ARG B:28 , HOH B:1062BINDING SITE FOR RESIDUE IPA B 861
13BC4SOFTWARETYR B:46 , SER B:47 , LEU B:49 , ALA B:82 , HOH B:1097 , HOH B:1247BINDING SITE FOR RESIDUE IPA B 862

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C1X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1C1X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C1X)

(-) Exons   (0, 0)

(no "Exon" information available for 1C1X)

(-) 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:348
 aligned with DHPH_RHOSO | Q59771 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:348
                                    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 SIDSALNWDGEMTVTRFDRETGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREA 349
               SCOP domains d1c1xa2 A:1-148 Phenylalanine dehydrogenase                                                                                                         d1c1xa1 A:149-348 Phenylalanine dehydrogenase                                                                                                                                                            SCOP domains
               CATH domains --1c1xA01 A:3-64,A:75-136,A:339-348                             ----------1c1xA01 A:3-64,A:75-136,A:339-348                             1c1xA02 A:137-338 NAD(P)-binding Rossmann-like Domain                                                                                                                                                     1c1xA01    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh....eeeeeee....eeeeeeeee.....ee..eeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhhhh...eeee.......hhhhhhhh...ee.........hhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c1x A   1 SIDSALNWDGEMTVTRFDSMTGAHFVIRLDSTQLGPAAGGTRAAQYSNLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREA 348
                                    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 d1c1xb2 B:1-148 Phenylalanine dehydrogenase                                                                                                         d1c1xb1 B:149-347 Phenylalanine dehydrogenase                                                                                                                                                           SCOP domains
               CATH domains --1c1xB01 B:3-64,B:75-136,B:339-347                             ----------1c1xB01 B:3-64,B:75-136,B:339-347                             1c1xB02 B:137-338 NAD(P)-binding Rossmann-like Domain                                                                                                                                                     1c1xB01   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....eeeeeee....eeeeeeeee.....ee..eeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhhhh...eeee.......hhhhhhhh...ee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c1x B   1 SIDSALNWDGEMTVTRFDKMTGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRARE 347
                                    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
   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 1C1X)

(-) 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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  1c1x
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  DHPH_RHOSO | Q59771
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHPH_RHOSO | Q59771: 1bw9 1bxg 1c1d

(-) Related Entries Specified in the PDB File

1bw9 L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND PHENYLPYRUVATE
1bxg L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND BETA- PHENYLPROPIONATE
1c1d L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L- PHENYLALANINE