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Title :   X-RAY STRUCTURE OF SHIKIMATE DEHYDROGENASE COMPLEXED WITH NAD+ FROM E.COLI (YDIB) NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER24

Authors :   J. Benach, A. P. Kuzin, I. Lee, B. Rost, Y. Chiang, T. B. Acton, G. T. Montelione, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   17 Jan 03 (Deposition) - 28 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Benach, I. Lee, W. Edstrom, A. P. Kuzin, Y. Chiang, T. B. Acton, G. T. Montelione, J. F. Hunt
The 2. 3-A Crystal Structure Of The Shikimate 5-Dehydrogenase Orthologue Ydib From Escherichia Coli Suggests A Novel Catalytic Environment For An Nad-Dependent Dehydrogenase
J. Biol. Chem. V. 278 19176 2003
PubMed-ID: 12624088 | Reference-DOI: 10.1074/JBC.M301348200
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL SHIKIMATE 5-DEHYDROGENASE-LIKE PROTEIN YDIB
	Chains	:	A, B
	EC Number	:	1.1.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMGK
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 24)

No.	Name	Count	Type	Full Name
1	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:107 , GLY A:131 , ALA A:132 , GLY A:133 , GLY A:134 , ALA A:135 , ASN A:155 , ARG A:156 , ASP A:158 , PHE A:160 , LEU A:184 , GLY A:203 , THR A:204 , LYS A:205 , VAL A:206 , MSE A:208 , CYS A:232 , VAL A:233 , TYR A:234 , ASN A:235 , GLY A:255 , MSE A:258 , LEU A:259 , HOH A:3013 , HOH A:3320 , HOH A:3321	BINDING SITE FOR RESIDUE NAD A 300
2	AC2	SOFTWARE	ASP B:107 , ALA B:132 , GLY B:133 , GLY B:134 , ALA B:135 , ASN B:155 , ARG B:156 , ASP B:158 , PHE B:160 , GLY B:203 , THR B:204 , LYS B:205 , VAL B:206 , MSE B:208 , CYS B:232 , TYR B:234 , GLY B:255 , MSE B:258 , LEU B:259 , HOH B:3014 , HOH B:3106 , HOH B:3111 , HOH B:3127 , HOH B:3271	BINDING SITE FOR RESIDUE NAD B 300

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:15	-	Pro A:16
2	Mse A:68	-	Pro A:69
3	Lys A:209	-	Pro A:210
4	Tyr B:15	-	Pro B:16
5	Mse B:68	-	Pro B:69
6	Lys B:209	-	Pro B:210
7	Asn B:235	-	Pro B:236

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

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

(no "Exon" information available for 1NPD)

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:287
 aligned with YDIB_ECOLI | P0A6D5 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    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       
           YDIB_ECOLI     1 MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFG 287
               SCOP domains d1npda2 A:1-106 Putative shikimate dehydrogenase YdiB                                                     d1npda1 A:107-287 Putative shikimate dehydrogenase YdiB                                                                                                                               SCOP domains
               CATH domains -1npdA01 A:2-107,A:259-287 Leucine Dehydrogenase, chain A, domain 1                                        1npdA02 A:108-257 NAD(P)-binding Rossmann-like Domain                                                                                                 -1npdA01 A:2-107,A:259-287     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeee.....hhhhhhh.eehhhhhhhh...eeeee..eeeeehhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhh...eeee................hhhhh....eeee.......hhhhhhhh.....eehhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npd A   1 mDVTAKYELIGLmAYPIRHSLSPEmQNKALEKAGLPFTYmAFEVDNDSFPGAIEGLKALKmRGTGVSmPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTmVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGmKPLENESLVNDISLLHPGLLVTECVYNPHmTKLLQQAQQAGCKTIDGYGmLLWQGAEQFTLWTGKDFPLEYVKQVmGFG 287
                            |       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   |   
                            |          13-MSE      25-MSE         40-MSE               61-MSE 68-MSE                                                    127-MSE                                                                          208-MSE                       238-MSE             258-MSE                   284-MSE
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with YDIB_ECOLI | P0A6D5 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:288
                                    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        
           YDIB_ECOLI     1 MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 288
               SCOP domains d1npdb2 B:1-106 Putative shikimate dehydrogenase YdiB                                                     d1npdb1 B:107-288 Putative shikimate dehydrogenase YdiB                                                                                                                                SCOP domains
               CATH domains -1npdB01 B:2-104,B:254-288 Leucine Dehydrogenase, chain A, domain 1                                     1npdB02 B:105-253 NAD(P)-binding Rossmann-like Domain                                                                                                1npdB01 B:2-104,B:254-288           CATH domains
           Pfam domains (1) -----------Shikimate_dh_N-1npdB03 B:12-94                                                     -------------------Shikimate_DH-1npdB01 B:114-230                                                                                       ---------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Shikimate_dh_N-1npdB04 B:12-94                                                     -------------------Shikimate_DH-1npdB02 B:114-230                                                                                       ---------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeeeee......hhhhhhhhhhhhh...eee..ee....hhhhhhhhhhhh...eeee.....hhhhhhh.eehhhhhhhh...eeeee..eeeeehhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh..eeee................hhhhh....eeee.......hhhhhhhhh...eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1npd B   1 mDVTAKYELIGLmAYPIRHSLSPEmQNKALEKAGLPFTYmAFEVDNDSFPGAIEGLKALKmRGTGVSmPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTmVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGmKPLENESLVNDISLLHPGLLVTECVYNPHmTKLLQQAQQAGCKTIDGYGmLLWQGAEQFTLWTGKDFPLEYVKQVmGFGA 288
                            |       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   |    
                            |          13-MSE      25-MSE         40-MSE               61-MSE 68-MSE                                                    127-MSE                                                                          208-MSE                       238-MSE             258-MSE                   284-MSE
                            1-MSE

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)

Escherichia coli. Organism_taxid: 562. (1)

1a	1npdB01	B:2-104,B:254-288
1b	1npdA01	A:2-107,A:259-287

Topology: Rossmann fold (7312)

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

Escherichia coli. Organism_taxid: 562. (49)

2a	1npdA02	A:108-257
2b	1npdB02	B:105-253

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Shikimate_DH (16)

Escherichia coli (strain K12) (3)

1a	Shikimate_DH-1npdB01	B:114-230
1b	Shikimate_DH-1npdB02	B:114-230

Clan: no clan defined [family: Shikimate_dh_N] (15)

Family: Shikimate_dh_N (15)

Escherichia coli (strain K12) (3)

2a	Shikimate_dh_N-1npdB03	B:12-94
2b	Shikimate_dh_N-1npdB04	B:12-94

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (YDIB_ECOLI | P0A6D5)

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:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	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:0030266	quinate 3-dehydrogenase (NAD+) activity	Catalysis of the reaction: (-)-quinate + NAD+ = (-)-3-dehydroquinate + NADH + H+.
	GO:0052733	quinate 3-dehydrogenase (NADP+) activity	Catalysis of the reaction: quinate + NADP+ = 3-dehydroquinate + NADPH + H+.
	GO:0052734	shikimate 3-dehydrogenase (NAD+) activity	Catalysis of the reaction: shikimate + NAD+ = 3-dehydroshikimate + NADH + H+.
	GO:0004764	shikimate 3-dehydrogenase (NADP+) activity	Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
biological process
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	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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	Cis Peptide Bonds
		Asn B:235 - Pro B:236	[ RasMol ]
		Lys A:209 - Pro A:210	[ RasMol ]
		Lys B:209 - Pro B:210	[ RasMol ]
		Mse A:68 - Pro A:69	[ RasMol ]
		Mse B:68 - Pro B:69	[ RasMol ]
		Tyr A:15 - Pro A:16	[ RasMol ]
		Tyr B:15 - Pro B:16	[ RasMol ]

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	1npd
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	YDIB_ECOLI \| P0A6D5
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	YDIB_ECOLI \| P0A6D5	:	1o9b 1vi2

aroe	NADP-DEPENDENT SHIKIMATE 5-DEHYDROGENASE
er24

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 24)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

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