3PQF - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM BACILLUS SUBTILIS MUTATION H171C COMPLEXED WITH NAD+

Authors :   Y. Zhang, R. M. Garavito

Date :   26 Nov 10 (Deposition) - 11 Jan 12 (Release) - 11 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.49

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

Keywords :   L-Lactate Dehydrogenase, Fbp, Nad+, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhang, R. M. Garavito
Crystal Structure Of L-Lactate Dehydrogenase From Bacillus Subtilis Mutation H171C Complexed With Nad+
To Be Published
PubMed: search

Molecule 1 - L-LACTATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLW01
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	T7 PROMOTER INDUCIBLE
	Gene	:	LDH, LCTE, BSU03050
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	L-LDH

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE C:11 , GLY C:14 , PHE C:15 , VAL C:16 , ASP C:37 , VAL C:38 , TYR C:68 , CYS C:80 , ALA C:81 , GLY C:82 , ALA C:83 , THR C:122 , THR C:232 , HOH C:332	BINDING SITE FOR RESIDUE NAD C 352
2	AC2	SOFTWARE	GLY D:14 , PHE D:15 , VAL D:16 , ASP D:37 , VAL D:38 , TYR D:68 , CYS D:80 , ALA D:81 , GLY D:82 , ALA D:83 , ILE D:101 , THR D:122 , THR D:232 , HOH D:327	BINDING SITE FOR RESIDUE NAD D 352

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

Asymmetric/Biological Unit

No.	Residues
1	Asn A:123	-	Pro A:124
2	Asn B:123	-	Pro B:124
3	Asn C:123	-	Pro C:124
4	Asn D:123	-	Pro D:124

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDH_BACSU	175-181	4	A:175-181 B:175-181 C:175-181 D:175-181

(no "Exon" information available for 3PQF)

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:314
 aligned with LDH_BACSU | P13714 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:314
                                    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       311    
            LDH_BACSU     2 NKHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVHAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHFA 315
               SCOP domains d3pqfa1 A:2-147 automated matches                                                                                                                 d3pqfa2 A:148-315 automated matches                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeeeehhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee..eeeee.hhh.eeeeee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pqf A   2 NKHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVCAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHFA 315
                                    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       311

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with LDH_BACSU | P13714 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:314
                                    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       311    
            LDH_BACSU     2 NKHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVHAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHFA 315
               SCOP domains d3pqfb1 B:2-147 automated matches                                                                                                                 d3pqfb2 B:148-315 automated matches                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeeeehhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee..eeeee.hhh.eeeeee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pqf B   2 NKHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVCAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHFA 315
                                    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       311

Chain C from PDB  Type:PROTEIN  Length:312
 aligned with LDH_BACSU | P13714 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
            LDH_BACSU     3 KHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVHAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHF 314
               SCOP domains d3pqfc1 C:3-147 automated matches                                                                                                                d3pqfc2 C:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..............hhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhh..hhh.ee..ee.......ee.hhh.ee..eehhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee..eeeee.....eeeeee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pqf C   3 KHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVCAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHF 314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

Chain D from PDB  Type:PROTEIN  Length:312
 aligned with LDH_BACSU | P13714 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
            LDH_BACSU     3 KHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVHAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHF 314
               SCOP domains d3pqfd1 D:3-147 automated matches                                                                                                                d3pqfd2 D:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhh..hhh.ee..ee.......ee.....ee..eehhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee..eeeee.....eeeeee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pqf D   3 KHVNKVALIGAGFVGSSYAFALINQGITDELVVIDVNKEKAMGDVMDLNHGKAFAPQPVKTSYGTYEDCKDADIVCICAGANQKPGETRLELVEKNLKIFKGIVSEVMASGFDGIFLVATNPVDILTYATWKFSGLPKERVIGSGTTLDSARFRFMLSEYFGAAPQNVCAHIIGEHGDTELPVWSHANVGGVPVSELVEKNDAYKQEELDQIVDDVKNAAYHIIEKKGATYYGVAMSLARITKAILHNENSILTVSTYLDGQYGADDVYIGVPAVVNRGGIAGITELNLNEKEKEQFLHSAGVLKNILKPHF 314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: LDH C-terminal domain-like (172)

Superfamily: LDH C-terminal domain-like (172)

Family: automated matches (38)

Protein domain: automated matches (38)

Bacillus subtilis [TaxId: 1423] (3)

1a	d3pqfa2	A:148-315
1b	d3pqfb2	B:148-315
1c	d3pqfc2	C:148-314
1d	d3pqfd2	D:148-314

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Bacillus subtilis [TaxId: 1423] (11)

2a	d3pqfa1	A:2-147
2b	d3pqfb1	B:2-147
2c	d3pqfc1	C:3-147
2d	d3pqfd1	D:3-147

(no "CATH Domain" information available for 3PQF)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (LDH_BACSU | P13714)

molecular function
	GO:0004459	L-lactate dehydrogenase activity	Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + 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:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:123 - Pro A:124	[ RasMol ]
		Asn B:123 - Pro B:124	[ RasMol ]
		Asn C:123 - Pro C:124	[ RasMol ]
		Asn D:123 - Pro D:124	[ RasMol ]

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	3pqf
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	LDH_BACSU \| P13714	:	3pqd 3pqe

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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