2V65 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   APO LDH FROM THE PSYCHROPHILE C. GUNNARI

Authors :   N. Coquelle, D. Madern, F. Vellieux

Date :   13 Jul 07 (Deposition) - 25 Sep 07 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (4x)
Biol. Unit 2: B  (4x)

Keywords :   Oxidoreductase, Lactate Dehydrogenase, Nad, Fish, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Coquelle, E. Fioravanti, M. Weik, F. Vellieux, D. Madern
Activity, Stability And Structural Studies Of Lactate Dehydrogenases Adapted To Extreme Thermal Environments.
J. Mol. Biol. V. 374 547 2007
PubMed-ID: 17936781 | Reference-DOI: 10.1016/J.JMB.2007.09.049

Molecule 1 - L-LACTATE DEHYDROGENASE A CHAIN
	Chains	:	A, B
	EC Number	:	1.1.1.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	469008
	Organism Common	:	MACKEREL ICEFISH
	Organism Scientific	:	CHAMPSOCEPHALUS GUNNARI
	Organism Taxid	:	52237
	Synonym	:	LDH-A
	Tissue	:	MUSCLE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A
Biological Unit 2 (4x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2V65)

(no "Site" information available for 2V65)

(no "SS Bond" information available for 2V65)

Asymmetric Unit

No.	Residues
1	Asn A:140	-	Pro A:141
2	Asn B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 2V65)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDHA_CHAGU	189-195	2	A:192-198 B:192-198

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.	LDHA_CHAGU	189-195	4	A:192-198 -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDHA_CHAGU	189-195	4	- B:192-198

(no "Exon" information available for 2V65)

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:326
 aligned with LDHA_CHAGU | O93541 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:330
                                    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       321       331
          LDHA_CHAGU      2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
               SCOP domains d2v65a1 A:2-162 automated matches                                                                                                                             d2v65a2 A:163-331 automated matches                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh..............eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh..eeee..hhhhhh...eeee....----..hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhhhee...................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2v65 A    2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGA----GESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
                                    11        22        32        42        52        62        72       |84        94     |   -|      115       125      |134       144       154       164       174       184       194       204    ||210B       220       230       240       250       260       270       280       290       301       311       321       331
                                             20|                                                        80|              100  106                      132A|                                                                         209A|||||                                                                                      299|                              
                                              22                                                         83                                             132B                                                                          209B||||                                                                                       301                              
                                                                                                                                                                                                                                       209C|||                                                                                                                        
                                                                                                                                                                                                                                        209D||                                                                                                                        
                                                                                                                                                                                                                                         210A|                                                                                                                        
                                                                                                                                                                                                                                          210B

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with LDHA_CHAGU | O93541 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:330
                                    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       321       331
          LDHA_CHAGU      2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
               SCOP domains d2v65b1 B:2-162 automated matches                                                                                                                             d2v65b2 B:163-331 automated matches                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------Ldh_1_N-2v65B03 B:22-163                                                                                                                    -Ldh_1_C-2v65B01 B:165-329                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) -------------------Ldh_1_N-2v65B04 B:22-163                                                                                                                    -Ldh_1_C-2v65B02 B:165-329                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author hhhhhhh..............eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh..eeee..hhhhhh...eeee....-----.hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhhhee...................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2v65 B    2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGA-----ESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
                                    11        22        32        42        52        62        72       |84        94     |   - |     115       125      |134       144       154       164       174       184       194       204    ||210B       220       230       240       250       260       270       280       290       301       311       321       331
                                             20|                                                        80|              100   107                     132A|                                                                         209A|||||                                                                                      299|                              
                                              22                                                         83                                             132B                                                                          209B||||                                                                                       301                              
                                                                                                                                                                                                                                       209C|||                                                                                                                        
                                                                                                                                                                                                                                        209D||                                                                                                                        
                                                                                                                                                                                                                                         210A|                                                                                                                        
                                                                                                                                                                                                                                          210B

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 "CATH Domain" information available for 2V65)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LDH_C (56)

Family: Ldh_1_C (51)

Champsocephalus gunnari (Mackerel icefish) (1)

1a	Ldh_1_C-2v65B01	B:165-329
1b	Ldh_1_C-2v65B02	B:165-329

Clan: NADP_Rossmann (1239)

Family: Ldh_1_N (51)

Champsocephalus gunnari (Mackerel icefish) (1)

2a	Ldh_1_N-2v65B03	B:22-163
2b	Ldh_1_N-2v65B04	B:22-163

Asymmetric Unit(hide GO term definitions)

Chain A,B (LDHA_CHAGU | O93541)

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: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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2v65)

	Sites
(no "Sites" information available for 2v65)

	Cis Peptide Bonds
		Asn A:140 - Pro A:141	[ RasMol ]
		Asn B:140 - Pro B:141	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2v65
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2v6b	LACTATE DEHYDROGENASE APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (8, 8)

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