1UXJ - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   LARGE IMPROVEMENT IN THE THERMAL STABILITY OF A TETRAMERIC MALATE DEHYDROGENASE BY SINGLE POINT MUTATIONS AT THE DIMER-DIMER INTERFACE

Authors :   A. Bjork, B. Dalhus, D. Mantzilas, V. G. H. Eijsink, R. Sirevag

Date :   25 Feb 04 (Deposition) - 26 Aug 04 (Release) - 15 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Oxidoreductase, Tricarboxylic Acid Cycle, Malate Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Bjork, B. Dalhus, D. Mantzilas, R. Sirevag, V. G. H. Eijsink
Large Improvement In The Thermal Stability Of A Tetrameric Malate Dehydrogenase By Single Point Mutations At The Dimer Dimer Interface.
J. Mol. Biol. V. 341 1215 2004
PubMed-ID: 15321717 | Reference-DOI: 10.1016/J.JMB.2004.06.079

Molecule 1 - MALATE DEHYDROGENASE
	Chains	:	A, C
	EC Number	:	1.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	CHLOROFLEXUS AURANTIACUS
	Organism Taxid	:	1108

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	CD	9	Ligand/Ion	CADMIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	NA	3	Ligand/Ion	SODIUM ION
4	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:200 , ASP A:243 , GLU A:277 , HOH A:2284	BINDING SITE FOR RESIDUE CD A1309
02	AC2	SOFTWARE	GLU A:195 , GLU A:281 , HOH A:2211 , GLU C:281 , HOH C:2278	BINDING SITE FOR RESIDUE CD A1310
03	AC3	SOFTWARE	GLU A:178 , CL A:1313 , HOH A:2154 , HOH A:2195	BINDING SITE FOR RESIDUE CD A1311
04	AC4	SOFTWARE	ASP A:148 , HIS A:175 , HOH A:2168 , HOH A:2172 , HOH A:2173	BINDING SITE FOR RESIDUE CD A1312
05	AC5	SOFTWARE	ASP A:123 , ALA A:124 , THR A:302 , CD A:1311	BINDING SITE FOR RESIDUE CL A1313
06	AC6	SOFTWARE	HIS A:19 , HOH A:2017	BINDING SITE FOR RESIDUE NA A1314
07	AC7	SOFTWARE	HOH A:2251	BINDING SITE FOR RESIDUE NA A1315
08	AC8	SOFTWARE	GLU C:178 , CL C:1314 , HOH C:2137 , HOH C:2181	BINDING SITE FOR RESIDUE CD C1311
09	AC9	SOFTWARE	GLU A:159 , ARG A:201 , HOH A:2181 , GLU C:159 , ARG C:201 , HOH C:2161	BINDING SITE FOR RESIDUE CD C1312
10	BC1	SOFTWARE	ASP C:148 , HIS C:175 , HOH C:2153 , HOH C:2176 , HOH C:2312	BINDING SITE FOR RESIDUE CD C1313
11	BC2	SOFTWARE	ASP C:123 , ALA C:124 , THR C:302 , CD C:1311	BINDING SITE FOR RESIDUE CL C1314
12	BC3	SOFTWARE	HOH A:2027 , GLU C:238	BINDING SITE FOR RESIDUE NA C1315
13	BC4	SOFTWARE	GLU A:238 , HOH A:2256 , HOH A:2257 , HOH C:2021 , HOH C:2168	BINDING SITE FOR RESIDUE CD C1316
14	BC5	SOFTWARE	HOH C:2085 , HOH C:2195 , HOH C:2251 , HOH C:2273 , HOH C:2275	BINDING SITE FOR RESIDUE CD C1317
15	BC6	SOFTWARE	GLY A:9 , GLY A:11 , PHE A:12 , VAL A:13 , ASP A:33 , ILE A:34 , VAL A:35 , TYR A:65 , THR A:77 , SER A:78 , GLY A:79 , PRO A:81 , CYS A:102 , VAL A:118 , ASN A:119 , ASN A:120 , GLN A:143 , LEU A:147 , HIS A:175 , PRO A:229 , HOH A:2118 , HOH A:2168 , HOH A:2248 , HOH A:2317 , HOH A:2318 , HOH A:2319 , HOH A:2320 , HOH A:2321 , HOH A:2322 , HOH A:2323 , HOH A:2324 , HOH A:2325	BINDING SITE FOR RESIDUE NAD A1308
16	BC7	SOFTWARE	GLY C:9 , GLY C:11 , PHE C:12 , VAL C:13 , ASP C:33 , ILE C:34 , VAL C:35 , TYR C:65 , THR C:77 , SER C:78 , GLY C:79 , ILE C:98 , CYS C:102 , VAL C:118 , ASN C:119 , ASN C:120 , GLN C:143 , LEU C:147 , HIS C:175 , PRO C:229 , HOH C:2096 , HOH C:2229 , HOH C:2230 , HOH C:2308 , HOH C:2310 , HOH C:2311 , HOH C:2312 , HOH C:2313 , HOH C:2314 , HOH C:2315	BINDING SITE FOR RESIDUE NAD C1310

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

Asymmetric Unit

No.	Residues
1	Asn A:120	-	Pro A:121
2	Asn C:120	-	Pro C:121

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

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

(no "Exon" information available for 1UXJ)

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:299
 aligned with MDH_CHLAA | P80040 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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        
            MDH_CHLAA     1 MRKKISIIGAGFVGSTTAHWLAAKELGDIVLLDFVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKS 308
               SCOP domains -d1uxja1 A:2-143 Malate dehydrogenase                                                                                                          d1uxja2 A:144-307 Malate dehydrogenase                                                                                                                              - SCOP domains
               CATH domains 1uxjA01 A:1-144 NAD(P)-binding Rossmann-like Domain                                                                                             1uxjA02 A:145-305 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                      --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.....---------hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eee..ee.hhh.ee.hhh.eee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uxj A   1 MRKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAP---------LIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVKDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKS 308
                                    10        20        30        40        50        60        70        80|        -|      100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                                                                           81        91

Chain C from PDB  Type:PROTEIN  Length:300
 aligned with MDH_CHLAA | P80040 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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        
            MDH_CHLAA     2 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDFVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGAPRKPGMSREDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVEDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKSL 309
               SCOP domains d1uxjc1 C:2-143 Malate dehydrogenase                                                                                                          d1uxjc2 C:144-307 Malate dehydrogenase                                                                                                                              -- SCOP domains
               CATH domains 1uxjC01 C:2-144 NAD(P)-binding Rossmann-like Domain                                                                                            1uxjC02 C:145-305 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                      ---- CATH domains
           Pfam domains (1) -Ldh_1_N-1uxjC03 C:3-143                                                                                                                      -Ldh_1_C-1uxjC01 C:145-309                                                                                                                                             Pfam domains (1)
           Pfam domains (2) -Ldh_1_N-1uxjC04 C:3-143                                                                                                                      -Ldh_1_C-1uxjC02 C:145-309                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee....--------hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eee..ee.hhh.ee.hhh.eee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uxj C   2 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTGTNNYADTANSDVIVVTSGA--------EDLIKVNADITRACISQAAPLSPNAVIIMVNNPLDAMTYLAAEVSGFPKERVIGQAGVLDAARYRTFIAMEAGVSVKDVQAMLMGGHGDEMVPLPRFSTISGIPVSEFIAPDRLAQIVERTRKGGGEIVNLLKTGSAYYAPAAATAQMVEAVLKDKKRVMPVAAYLTGQYGLNDIYFGVPVILGAGGVEKILELPLNEEEMALLNASAKAVRATLDTLKSL 309
                                    11        21        31        41        51        61        71        |-       |91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
                                                                                                         80       89

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LDH_C (56)

Family: Ldh_1_C (51)

Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (6)

1a	Ldh_1_C-1uxjC01	C:145-309
1b	Ldh_1_C-1uxjC02	C:145-309

Clan: NADP_Rossmann (1239)

Family: Ldh_1_N (51)

Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (6)

2a	Ldh_1_N-1uxjC03	C:3-143
2b	Ldh_1_N-1uxjC04	C:3-143

Asymmetric Unit(hide GO term definitions)

Chain A,C (MDH_CHLAA | P80040)

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: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: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 Unit
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	Cis Peptide Bonds
		Asn A:120 - Pro A:121	[ RasMol ]
		Asn C:120 - Pro C:121	[ RasMol ]

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	1uxj
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	1.1.1.37
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UniProtKB/Swiss-Prot
	MDH_CHLAA \| P80040	:	1guy 1ur5 1uxg 1uxh 1uxi 1uxk 4cl3

1guy	STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
1ur5	STABILIZATION OF A TETRAMERIC MALATE DEHYDROGENASE BY INTRODUCTION OF A DISULFIDE BRIDGE AT THE DIMER-DIMER INTERFACE
1uxg	STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
1uxh	STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
1uxi	STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES
1uxk	STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (2, 4)

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Pfam Domains (2, 4)

Gene Ontology (8, 8)

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