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Title :   CRYSTAL STRUCTURE OF TARTRATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH NADH

Authors :   R. Malik, R. E. Viola

Date :   22 Dec 08 (Deposition) - 12 Jan 10 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : X
Biol. Unit 1: X  (4x)
Biol. Unit 2: X  (2x)

Keywords :   Oxidoreductase, Lyase, Magnesium, Manganese, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Malik, R. E. Viola
Structural Characterization Of Tartrate Dehydrogenase: A Versatile Enzyme Catalyzing Multiple Reactions
To Be Published
PubMed: search

Molecule 1 - TARTRATE DEHYDROGENASE/DECARBOXYLASE
	Chains	:	X
	EC Number	:	1.1.1.93, 4.1.1.73, 1.1.1.83
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 3A
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TTUC
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	TDH, D-MALATE DEHYDROGENASE [DECARBOXYLATING]

		1
Asymmetric Unit	:	X
Biological Unit 1 (4x)	:	X
Biological Unit 2 (2x)	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	NAI	1	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	NH4	1	Ligand/Ion	AMMONIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	NAI	4	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	NH4	4	Ligand/Ion	AMMONIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	NH4	2	Ligand/Ion	AMMONIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE X:75 , ALA X:77 , VAL X:78 , GLY X:79 , ASP X:86 , LEU X:94 , ASN X:194 , ILE X:226 , ARG X:230 , ILE X:263 , GLY X:264 , GLU X:282 , HIS X:285 , GLY X:286 , SER X:287 , ALA X:288 , ASP X:290 , ILE X:291 , ASN X:298 , ASP X:343 , NH4 X:402	BINDING SITE FOR RESIDUE NAI X 401
2	AC2	SOFTWARE	GLY X:76 , GLU X:282 , PRO X:283 , HIS X:285 , NAI X:401	BINDING SITE FOR RESIDUE NH4 X 402

(no "SS Bond" information available for 3FMX)

(no "Cis Peptide Bond" information available for 3FMX)

(no "SAP(SNP)/Variant" information available for 3FMX)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	TTUC_PSEPU	246-265	1	X:246-265

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	TTUC_PSEPU	246-265	4	X:246-265

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	TTUC_PSEPU	246-265	2	X:246-265

(no "Exon" information available for 3FMX)

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 X from PDB  Type:PROTEIN  Length:359
 aligned with TTUC_PSEPU | Q51945 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:360
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
           TTUC_PSEPU     5 SFRIAAIPGDGIGLEVLPEGIRVLEAAALKHGLALEFDTFEWASCDYYLQHGKMMPDDWAEQLKQYDAIYFGAVDWPDKVPDHISLWGSLLKFRREFDQYVNIRPVRLFPGVPCALANRKVGDIDFVVVRENTEGEYSSLGGIMFENTENEIVIQESIFTRRGVDRILKYAFDLAEKRERKHVTSATKSNGMAISMPYWDKRTEAMAAHYPHVSWDKQHIDILCARFVLQPERFDVVVVASNLFGDILSDLGPACAGTIGIAPSANLNPERNFPSLFEPVHGSAPDIFGKNIANPIAMIWSGALMLEFLGQGDERYQRAHDDMLNAIERVIADGSVTPDMGGTLSTQQVGAAISDTLARL 364
               SCOP domains d3fmxx_ X: automated matches                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3fmxX00 X:5-364 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..ee.......hhhhhhhhh.....hhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh...eee..ee.................eeeeeee.........eeee.......eeee....hhhhhhhhhhh...........eeeeee......hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhh.....eee-e.hhhhhh..........hhhh.eeeee.......eeeee....hhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fmx X   5 SFRIAAIPGDGIGLEVLPEGIRVLEAAALKHGLALEFDTFEWASCDYYLQHGKMMPDDWAEQLKQYDAIYFGAVGWPDKVPDHISLWGSLLKFRREFDQYVNIRPVRLFPGVPCALANRKVGDIDFVVVRENTEGEYSSLGGIMFENTENEIVIQESIFTRRGVDRILKYAFDLAEKRERKHVTSATKSNGMAISMPYWDKRTEAMAAHYPHVSWDKQHIDILCARFVLQPERFDVVV-ASNLFGDILSDLGPACAGTIGIAPSANLNPERNFPSLFEPVHGSAPDIFGKNIANPIAMIWSGALMLEFLGQGDERYQRAHDDMLNAIERVIADGSVTPDMGGTLSTQQVGAAISDTLARL 364
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
                                                                                                                                                                                                                                                                       242 |                                                                                                                        
                                                                                                                                                                                                                                                                         244

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Family: automated matches (22)

Protein domain: automated matches (22)

Pseudomonas putida [TaxId: 303] (2)

d3fmxx_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Pseudomonas putida. Organism_taxid: 303. (1)

3fmxX00

X:5-364

(no "Pfam Domain" information available for 3FMX)

Asymmetric Unit(hide GO term definitions)

Chain X (TTUC_PSEPU | Q51945)

molecular function
	GO:0046553	D-malate dehydrogenase (decarboxylating) activity	Catalysis of the reaction: (R)-malate + NAD(+) = CO(2) + NADH + pyruvate.
	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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0050319	tartrate decarboxylase activity	Catalysis of the reaction: L-tartrate + H(+) = D-glycerate + CO(2).
	GO:0009027	tartrate dehydrogenase activity	Catalysis of the reaction: tartrate + NAD+ = oxaloglycolate + NADH + H+.
biological process
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	TTUC_PSEPU \| Q51945	:	3flk

3flk	COMPLEX WITH INTERMEDIATE ANALOG (OXALATE), NADH AND DIVALENT METAL ION

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