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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY

Authors :   C. A. Kelly, J. J. Birktoft

Date :   16 Feb 93 (Deposition) - 20 Dec 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Oxidoreductase(Nad(A)-Choh(D)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Kelly, M. Nishiyama, Y. Ohnishi, T. Beppu, J. J. Birktoft
Determinants Of Protein Thermostability Observed In The 1. 9-A Crystal Structure Of Malate Dehydrogenase From The Thermophilic Bacterium Thermus Flavus.
Biochemistry V. 32 3913 1993
PubMed-ID: 8471603 | Reference-DOI: 10.1021/BI00066A010
(for further references see the PDB file header)

Molecule 1 - MALATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.37
	Engineered	:	YES
	Expression System Vector Type	:	BACTERIUM
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAX	2	Ligand/Ion	BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINEDINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:10 , GLY A:13 , GLN A:14 , ILE A:15 , GLU A:41 , ILE A:42 , VAL A:86 , GLY A:87 , ALA A:88 , GLN A:111 , VAL A:128 , GLY A:129 , ASN A:130 , MET A:154 , HIS A:186 , ALA A:245 , HOH A:767 , HOH A:795 , HOH A:904 , HOH A:907 , HOH A:913 , HOH A:916 , HOH A:950	BINDING SITE FOR RESIDUE NAX A 334
2	AC2	SOFTWARE	GLY B:10 , GLY B:13 , GLN B:14 , ILE B:15 , GLU B:41 , ILE B:42 , VAL B:86 , GLY B:87 , ALA B:88 , ILE B:107 , GLN B:111 , VAL B:128 , GLY B:129 , ASN B:130 , MET B:154 , HIS B:186 , ALA B:245 , HOH B:765 , HOH B:784 , HOH B:866 , HOH B:922 , HOH B:933	BINDING SITE FOR RESIDUE NAX B 334

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

Asymmetric/Biological Unit

No.	Residues
1	Asn A:130	-	Pro A:131
2	Asn B:130	-	Pro B:131

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MDH_THETH_001 *	T	190	I	MDH_THETH	---	---	A/B	I	189	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDH_THETH	155-167	2	A:154-166 B:154-166

(no "Exon" information available for 1BDM)

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:318
 aligned with MDH_THETH | P10584 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:327
                                    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       
            MDH_THETH     1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI 327
               SCOP domains d1bdma1 A:0-154 Malate dehydrogenase                                                                                                                       d1bdma2 A:155-332 Malate dehydrogenase                                                                                                                                       SCOP domains
               CATH domains -1bdmA01 A:1-153 NAD(P)-binding Rossmann-like Domain                                                                                                      1bdmA02 A:154-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhh..........eeeeee..hhhhhhhhhhhhhhh......eeeeeee..hhhh.....eeee......---------hhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhh.........eee..hhhhhhhhhhhhhhh......eeeeeee.......eeeeeeeee..eehhhhh.hhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhh........eeeeee...........eeeeeeeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdm A   0 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPDVAFKDADYALLVGAAPR---------LQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI 332
                                     9        19        29        39        49        59        69        79        89 |       - |     109       119       129       139       149       159       169       179       189       199||     214       224       234       244       254       264       274||     285       295       305       315       325       
                                                                                                                      91       101                                                                                                200|    212|                                                          275|                                                       
                                                                                                                                                                                                                                   205     214                                                           277

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with MDH_THETH | P10584 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:327
                                    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       
            MDH_THETH     1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI 327
               SCOP domains d1bdmb1 B:0-154 Malate dehydrogenase                                                                                                                       d1bdmb2 B:155-332 Malate dehydrogenase                                                                                                                                       SCOP domains
               CATH domains -1bdmB01 B:1-153 NAD(P)-binding Rossmann-like Domain                                                                                                      1bdmB02 B:154-332 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhh..........eeeeee..hhhhhhhhhhhhhhh......eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhh.........eee..hhhhhhhhhhhhhhh......eeeeeee.......eeeeeeeee..eehhhhh.hhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhh.......eeeeee...........eeeeeeeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdm B   0 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPDVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI 332
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199||     214       224       234       244       254       264       274||     285       295       305       315       325       
                                                                                                                                                                                                                                  200|    212|                                                          275|                                                       
                                                                                                                                                                                                                                   205     214                                                           277

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 "Pfam Domain" information available for 1BDM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MDH_THETH | P10584)

molecular function
	GO:0030060	L-malate dehydrogenase activity	Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
	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:0016615	malate dehydrogenase activity	Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
	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.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006108	malate metabolic process	The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
	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:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Asymmetric/Biological Unit
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		Asn B:130 - Pro B:131	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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