2O7S - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE A. THALIANA DHQ-DEHYDROSHIKIMATE-SDH-SHIKIMATE-NADP(H)

Authors :   D. Christendat, S. A. Singh

Date :   11 Dec 06 (Deposition) - 20 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Shikimate; Nadph; Dehydroshikimate; Bifunctional Enzyme, Oxidoreductase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Singh, D. Christendat
The Dhq-Dehydroshikimate-Sdh-Shikimate-Nadp(H) Complex: Insights Into Metabolite Transfer In The Shikimate Pathway
Cryst. Growth Des. V. 7 2153 2007
PubMed: search | Reference-DOI: 10.1021/CG7007107

Molecule 1 - BIFUNCTIONAL 3-DEHYDROQUINATE DEHYDRATASE/SHIKIMATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.1.1.25, 4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28 WITH C-TERMINAL HIS TAG
	Expression System Strain	:	BL21-CODON+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	EMB3004
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Other Details	:	CONTAINS DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10) AND SHIKIMATE DEHYDROGENASE (EC 1.1.1.25)
	Strain	:	COLUMBIA-0
	Synonym	:	DEHYDROQUINASE-SHIKIMATE DEHYDROGENASE; DHQ-SDH PROTEIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 7)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	DHK	2	Ligand/Ion	3-DEHYDROSHIKIMATE
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	SO4	1	Ligand/Ion	SULFATE ION
5	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (5, 7)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	DHK	2	Ligand/Ion	3-DEHYDROSHIKIMATE
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	SO4	1	Ligand/Ion	SULFATE ION
5	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (5, 14)

No.	Name	Count	Type	Full Name
1	CSO	4	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	DHK	4	Ligand/Ion	3-DEHYDROSHIKIMATE
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	SO4	2	Ligand/Ion	SULFATE ION
5	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:158 , SER A:334 , PRO A:527 , HOH A:9246	BINDING SITE FOR RESIDUE SO4 A 1403
2	AC2	SOFTWARE	GLU A:124 , ARG A:126 , ARG A:155 , LYS A:241 , ARG A:279 , PHE A:291 , SER A:300 , ALA A:301 , GLN A:304 , HOH A:9258	BINDING SITE FOR RESIDUE DHK A 9241
3	AC3	SOFTWARE	ARG A:155 , HIS A:214 , LYS A:241 , LEU A:269 , MET A:271 , ARG A:279 , PHE A:291 , ALA A:301 , GLN A:304 , HOH A:9349	BINDING SITE FOR RESIDUE TLA A 1241
4	AC4	SOFTWARE	ILE A:328 , SER A:336 , SER A:338 , SER A:379 , THR A:381 , LYS A:385 , ASN A:406 , ASP A:423 , TYR A:550 , GLN A:578 , GLN A:582 , NAP A:1411 , HOH A:9267	BINDING SITE FOR RESIDUE DHK A 4733
5	AC5	SOFTWARE	ILE A:382 , PRO A:383 , LYS A:385 , ASP A:423 , GLY A:460 , ALA A:461 , GLY A:462 , GLY A:463 , ALA A:464 , ASN A:483 , ARG A:484 , THR A:485 , ARG A:488 , THR A:520 , THR A:521 , SER A:522 , MET A:523 , MET A:525 , ALA A:548 , TYR A:550 , GLY A:571 , MET A:574 , PHE A:575 , GLN A:578 , DHK A:4733 , HOH A:9263 , HOH A:9267 , HOH A:9328	BINDING SITE FOR RESIDUE NAP A 1411

(no "SS Bond" information available for 2O7S)

Asymmetric Unit

No.	Residues
1	Lys A:331	-	Pro A:332
2	Ile A:382	-	Pro A:383
3	Gln A:526	-	Pro A:527
4	Thr A:551	-	Pro A:552

(no "SAP(SNP)/Variant" information available for 2O7S)

(no "PROSITE Motif" information available for 2O7S)

(no "Exon" information available for 2O7S)

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:500
 aligned with DHQSD_ARATH | Q9SQT8 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:523
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           603         
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599   |     -   
          DHQSD_ARATH    90 VKNPSLICAPVMADSIDKMVIETSKAHELGADLVEIRLDWLKDFNPLEDLKTIIKKSPLPTLFTYRPKWEGGQYEGDENERRDVLRLAMELGADYIDVELQVASEFIKSIDGKKPGKFKVIVSSHNYQNTPSVEDLDGLVARIQQTGADIVKIATTAVDIADVARMFHITSKAQVPTIGLVMGERGLMSRILCSKFGGYLTFGTLDSSKVSAPGQPTIKDLLDLYNFRRIGPDTKVYGIIGKPVSHSKSPIVHNQAFKSVDFNGVYVHLLVDNLVSFLQAYSSSDFAGFSCTIPHKEAALQCCDEVDPLAKSIGAVNTILRRKSDGKLLGYNTDCIGSISAIEDGLRSSGDPSSVPSSSSPLASKTVVVIGAGGAGKALAYGAKEKGAKVVIANRTYERALELAEAIGGKALSLTDLDNYHPEDGMVLANTTSMGMQPNVEETPISKDALKHYALVFDAVYTPRITRLLREAEESGAITVSGSEMFVRQAYEQFEIFTGLPAPKELYWQIMSKY---------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------DHquinase_I-2o7sA02 A:97-315                                                                                                                                                                                               ------------Shikimate_dh_N-2o7sA03 A:328-408                                                 ---------------------------                   Shikimate_DH-2o7sA01 A: 455-570                                                                                     ------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee...hhhhhhhhhhhhhhhh..eeeee.hhh...hhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh........eeeeeee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhh.......eee..............hhhhhhhh.hhhhh....eeeeeee......hhhhhhhhhhhhh...eeeeeee..hhhhhhhhh....eeeeee...hhhhhhhhh.eehhhhhhhh...eeee......eeee.hhhhhhhhhhhhhh-------------------.eeee..hhhhhhhhhhhhhhh.-.eeee.hhhhhhhhhhhh..-.ee.......--...eeeee..................hhh.eeeeee.......hhhhhhhhh...eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o7s A  90 VKNPSLICAPVMADSIDKMVIETSKAHELGADLVEIRLDWLKDFNPLEDLKTIIKKSPLPTLFTYRPKWEGGQYEGDENERRDVLRLAMELGADYIDVELQVASEFIKSIDGKKPGKFKVIVSSHNYQNTPSVEDLDGLVARIQQTGADIVKIATTAVDIADVARMFHITSKAQVPTIGLVMGERGLMSRILCSKFGGYLTFGTLDSSKVSAPGQPTIKDLLDLYNFRRIGPDTKVYGIIGKPVSHSKSPIVHNQAFKSVDFNGVYVHLLVDNLVSFLQAYSSSDFAGFSCTIPHKEAALQcCDEVDPLAKSIGAVNTILRRKSDGKLLGYNTDcIGSISAIEDGL-------------------TVVVIGAGGAGKALAYGAKEKGA-VVIANRTYERALELAEAIGG-ALSLTDLDNY--EDGMVLANTTSMGMQPNVEETPISKDALKHYALVFDAVYTPRITRLLREAEESGAITVSGSEMFVRQAYEQFEIFTGLPAPKELYWQIMSKYGSRENLYFQ 612
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389 |     399       409       419    |  429     |   -         -     | 459       469       479       489        |-|      509  |    519       529       539       549       559       569       579       589       599       609   
                                                                                                                                                                                                                                                                                                                                       391-CSO                          424-CSO    435                 455                   477 |                498 |      509  |                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                               479                  500         512

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 '\|'

(no "SCOP Domain" information available for 2O7S)

(no "CATH Domain" information available for 2O7S)

Asymmetric Unit(hide GO term definitions)

Chain A (DHQSD_ARATH | Q9SQT8)

molecular function
	GO:0003855	3-dehydroquinate dehydratase activity	Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
	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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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: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:0009793	embryo development ending in seed dormancy	The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
	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.
	GO:0019632	shikimate metabolic process	The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009570	chloroplast stroma	The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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	Cis Peptide Bonds
		Gln A:526 - Pro A:527	[ RasMol ]
		Ile A:382 - Pro A:383	[ RasMol ]
		Lys A:331 - Pro A:332	[ RasMol ]
		Thr A:551 - Pro A:552	[ RasMol ]

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	DHQSD_ARATH \| Q9SQT8	:	2gpt 2o7q

2gpt	DHQ-TARTRATE-SDH-SHIKIMATE CO-COMPLEXES
2o7s

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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