1C1D - JenaLib

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Title :   L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE

Authors :   J. L. Vanhooke, J. B. Thoden

Date :   21 Jul 99 (Deposition) - 30 Aug 00 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

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

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 - L-PHENYLALANINE DEHYDROGENASE
	Chains	:	B
	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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 12)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
2	K	4	Ligand/Ion	POTASSIUM ION
3	NA	2	Ligand/Ion	SODIUM ION
4	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
5	PHE	2	Mod. Amino Acid	PHENYLALANINE
6	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:118 , THR A:121 , HOH A:1493 , HOH A:1602	BINDING SITE FOR RESIDUE K A 850
02	AC2	SOFTWARE	LEU B:170 , SER B:172 , ASP B:174 , LEU B:176 , PO4 B:880 , HOH B:1194 , HOH B:1421	BINDING SITE FOR RESIDUE K B 851
03	AC3	SOFTWARE	ASP B:118 , THR B:121 , HOH B:1320 , HOH B:1452 , HOH B:1667 , HOH B:1746	BINDING SITE FOR RESIDUE K B 852
04	AC4	SOFTWARE	VAL A:136 , PHE A:137 , GLY A:138 , ARG A:139 , GLY A:145 , GLU A:299	BINDING SITE FOR RESIDUE K A 853
05	AC5	SOFTWARE	ASP B:30 , HOH B:1094 , HOH B:1140	BINDING SITE FOR RESIDUE NA B 854
06	AC6	SOFTWARE	GLN B:200 , LEU B:201 , HIS B:219 , HOH B:1067 , HOH B:1754	BINDING SITE FOR RESIDUE NA B 855
07	AC7	SOFTWARE	SER B:1 , SER B:4 , THR B:54 , LYS B:58 , LEU B:170 , LEU B:176 , K B:851 , HOH B:1106 , HOH B:1168 , HOH B:1421 , HOH B:1456 , HOH B:1510	BINDING SITE FOR RESIDUE PO4 B 880
08	AC8	SOFTWARE	GLY A:39 , GLY A:40 , LYS A:66 , LYS A:78 , PRO A:117 , ASP A:118 , ASN A:262 , ALA A:292 , LEU A:295 , NAI A:360 , HOH A:1046 , HOH A:1226	BINDING SITE FOR RESIDUE PHE A 361
09	AC9	SOFTWARE	GLY B:39 , GLY B:40 , MET B:63 , LYS B:66 , LYS B:78 , PRO B:117 , ASP B:118 , ASN B:262 , NAI B:760 , HOH B:1008 , HOH B:1073	BINDING SITE FOR RESIDUE PHE B 761
10	BC1	SOFTWARE	ARG A:42 , ASP 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 , LEU A:224 , CYS A:238 , ALA A:239 , ALA A:260 , ALA A:261 , ASN A:262 , ASN A:288 , PHE A:361 , HOH A:1082 , HOH A:1149 , HOH A:1163 , HOH A:1281 , HOH A:1488 , HOH A:1493 , HOH A:1786 , HOH A:1867	BINDING SITE FOR RESIDUE NAI A 360
11	BC2	SOFTWARE	ARG B:42 , ASP B:118 , SER B:149 , THR B:153 , GLY B:182 , LEU B:183 , 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 , PHE B:761 , HOH B:1091 , HOH B:1123 , HOH B:1300 , HOH B:1320 , HOH B:1498	BINDING SITE FOR RESIDUE NAI B 760
12	BC3	SOFTWARE	THR A:15 , ARG B:28 , HOH B:1062	BINDING SITE FOR RESIDUE IPA B 860

(no "SS Bond" information available for 1C1D)

(no "Cis Peptide Bond" information available for 1C1D)

(no "SAP(SNP)/Variant" information available for 1C1D)

(no "PROSITE Motif" information available for 1C1D)

(no "Exon" information available for 1C1D)

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 d1c1da2 A:1-148 Phenylalanine dehydrogenase                                                                                                         d1c1da1 A:149-349 Phenylalanine dehydrogenase                                                                                                                                                             SCOP domains
               CATH domains --1c1dA01 A:3-64,A:75-136,A:339-349                             ----------1c1dA01 A:3-64,A:75-136,A:339-349                             1c1dA02 A:137-338 NAD(P)-binding Rossmann-like Domain                                                                                                                                                     1c1dA01     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....eeeeeee....eeeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhhhh...eeee.......hhhhhhhh...ee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c1d A   1 SIDSALNWDGEMTVTRFDAMTGAHFVIRLDSTQLGPAAGGTRAAQYSNLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREAS 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: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 d1c1db2 B:1-148 Phenylalanine dehydrogenase                                                                                                         d1c1db1 B:149-348 Phenylalanine dehydrogenase                                                                                                                                                            SCOP domains
               CATH domains --1c1dB01 B:3-64,B:75-136,B:339-348                             ----------1c1dB01 B:3-64,B:75-136,B:339-348                             1c1dB02 B:137-338 NAD(P)-binding Rossmann-like Domain                                                                                                                                                     1c1dB01    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.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c1d B   1 SIDSALNWDGEMTVTRFDSMTGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREA 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

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Leucine Dehydrogenase; Chain A, domain 1 (52)

Homologous Superfamily: Leucine Dehydrogenase, chain A, domain 1 (52)

Rhodococcus sp.. Organism_taxid: 1831. (2)

1a	1c1dA01	A:3-64,A:75-136,A:339-349
1b	1c1dB01	B:3-64,B:75-136,B:339-348

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Rhodococcus sp.. Organism_taxid: 1831. (2)

2a	1c1dA02	A:137-338
2b	1c1dB02	B:137-338

(no "Pfam Domain" information available for 1C1D)

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.

Asymmetric/Biological Unit
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	1c1d
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	DHPH_RHOSO \| Q59771	:	1bw9 1bxg 1c1x

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (2, 4)

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Gene Ontology (8, 8)

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