3D4P - JenaLib

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Title :   CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM STAPHYLOCOCCUS AUREUS COMPLEXED WITH NAD AND PYRUVATE

Authors :   V. L. Schramm, S. C. Almo, J. A. Gutierrez, M. Ho

Date :   14 May 08 (Deposition) - 02 Jun 09 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B  (2x)

Keywords :   Lactate Dehydrogenase, Staphylococcus Aureus, Nad, Pyruvate, Cytoplasm, Glycolysis, Oxidoreductase, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. L. Schramm, S. C. Almo, J. A. Gutierrez, M. Ho
Crystal Structure Of Lactate Dehydrogenase From Staphylococcus Aureus Complexed With Nad And Pyruvate
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - L-LACTATE DEHYDROGENASE 1
	Chains	:	A, B
	EC Number	:	1.1.1.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	LDH1, SACOL0222
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL
	Organism Taxid	:	93062
	Synonym	:	L-LDH 1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

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

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	PYR	4	Ligand/Ion	PYRUVIC ACID

Biological Unit 2 (2, 4)

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

Biological Unit 3 (2, 4)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , ALA A:16 , ASP A:38 , LEU A:39 , CYS A:81 , ALA A:82 , GLY A:83 , ALA A:84 , ALA A:122 , THR A:123 , ASN A:124 , SER A:147 , LEU A:151 , HIS A:179 , THR A:232	BINDING SITE FOR RESIDUE NAD A 318
2	AC2	SOFTWARE	ASN A:124 , LEU A:151 , ARG A:155 , HIS A:179 , ALA A:222 , THR A:232	BINDING SITE FOR RESIDUE PYR A 319
3	AC3	SOFTWARE	GLY B:15 , ALA B:16 , ASP B:38 , LEU B:39 , CYS B:81 , ALA B:82 , GLY B:83 , ALA B:84 , ALA B:122 , THR B:123 , ASN B:124 , SER B:147 , LEU B:151 , HIS B:179 , THR B:232	BINDING SITE FOR RESIDUE NAD B 318
4	AC4	SOFTWARE	ASN B:124 , LEU B:151 , ARG B:155 , HIS B:179 , ALA B:222 , THR B:232	BINDING SITE FOR RESIDUE PYR B 319

(no "SS Bond" information available for 3D4P)

Asymmetric Unit

No.	Residues
1	Asn A:124	-	Pro A:125
2	Asn B:124	-	Pro B:125

(no "SAP(SNP)/Variant" information available for 3D4P)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDH1_STAAC	176-182	2	A:176-182 B:176-182

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDH1_STAAC	176-182	4	A:176-182 B:176-182

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDH1_STAAC	176-182	2	A:176-182 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDH1_STAAC	176-182	2	- B:176-182

(no "Exon" information available for 3D4P)

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:307
 aligned with LDH1_STAAC | Q5HJD7 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
           LDH1_STAAC     4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAE 312
               SCOP domains d3d4pa1 A:4-148 automated matches                                                                                                                d3d4pa2 A:149-312 automated matches                                                                                                                                  SCOP domains
               CATH domains 3d4pA01 A:4-148 NAD(P)-binding Rossmann-like Domain                                                                                              3d4pA02 A:149-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee........--hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh...ee.......ee.....ee..eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4p A   4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKP--TRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAE 312
                                    13        23        33        43        53        63        73        83    |  |93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
                                                                                                               88 91

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with LDH1_STAAC | Q5HJD7 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
           LDH1_STAAC     4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAEA 313
               SCOP domains d3d4pb1 B:4-148 automated matches                                                                                                                d3d4pb2 B:149-313 automated matches                                                                                                                                   SCOP domains
               CATH domains 3d4pB01 B:4-148 NAD(P)-binding Rossmann-like Domain                                                                                              3d4pB02 B:149-313 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh...ee.......ee.....ee..eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4p B   4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAEA 313
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

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 3D4P)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LDH1_STAAC | Q5HJD7)

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 Unit
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	3d4p
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	LDH1_STAAC \| Q5HJD7	:	3d0o 3h3j

3d0o	THE SAME PROTEIN COMPLEXED WITH NAD AND PYRUVATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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