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(-) Description

Title :  STRUCTURAL FEATURES STABILIZING HALOPHILIC MALATE DEHYDROGENASE FROM AN ARCHAEBACTERIUM
 
Authors :  O. Dym, M. Mevarech, J. L. Sussman
Date :  04 Oct 94  (Deposition) - 26 Jan 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Halophilic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Dym, M. Mevarech, J. L. Sussman
Structural Features That Stabilize Halophilic Malate Dehydrogenase From An Archaebacterium.
Science V. 267 1344 1995
PubMed-ID: 17812611  |  Reference-DOI: 10.1126/SCIENCE.267.5202.1344
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11D
    Expression System Taxid: 562
    Organism Scientific: HALOARCULA MARISMORTUI
    Organism Taxid: 2238

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:27 , ALA A:28 , GLY A:29 , THR A:30 , VAL A:31 , ASP A:52 , ILE A:53 , LYS A:54 , TYR A:83 , THR A:95 , ALA A:96 , ILE A:120 , THR A:136 , ASN A:138 , VAL A:140 , PHE A:161 , GLY A:162 , LEU A:165 , HIS A:193 , THR A:245 , PRO A:249BINDING SITE FOR RESIDUE NAD A 330
2AC2SOFTWAREGLY B:27 , ALA B:28 , GLY B:29 , THR B:30 , VAL B:31 , ASP B:52 , ILE B:53 , LYS B:54 , TYR B:83 , THR B:95 , ILE B:120 , THR B:136 , ASN B:138 , VAL B:140 , PHE B:161 , GLY B:162 , LEU B:165 , HIS B:193 , THR B:245BINDING SITE FOR RESIDUE NAD B 330

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HLP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1HLP)

(-) Sequences/Alignments

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:303
 aligned with MDH_HALMA | Q07841 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    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_HALMA     2 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS 304
               SCOP domains d1hlpa1 A:21-162 Malate dehydrogenase                                                                                                           d1hlpa2 A:163-328 Malate dehydrogenase                                                                                                                          SCOP domains
               CATH domains 1hlpA02 A:21-160 NAD(P)-binding Rossmann-like Domain                                                                                          1hlpA01 A:161-328 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh...eeeee...hhh.hhhhhhhhhhhhhh....eee............eeee...........hhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..hhh.eee.hhhhhhhhhhhhhhhhhh.........eee.....eee.hhhh............hhhhhhhhhhh............hhhhhhhhhhhhhhhhh....eeeee..eee...eeee..eeeee.......ee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hlp A  21 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS 328
                                   |29        39        49    ||  57        67   ||   78        88        98       108       118       128       138       148       158       168       178       188       198       208  ||   224       234       244       254       264       274    || 285       295       305       315       325   
                                 27A                        53A|                71|                                                                                                                                       211|                                                          279|                                               
                                                             53B                 73                                                                                                                                        218                                                           281                                               


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with MDH_HALMA | Q07841 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    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_HALMA     2 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS 304
               SCOP domains d1hlpb1 B:21-162 Malate dehydrogenase                                                                                                           d1hlpb2 B:163-328 Malate dehydrogenase                                                                                                                          SCOP domains
               CATH domains 1hlpB02 B:21-160 NAD(P)-binding Rossmann-like Domain                                                                                          1hlpB01 B:161-328 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhh...eeeee..hhhh.hhhhhhhhhhhhhh....ee....hhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhh.........eee.....eee.hhhh............hhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhh....eeeeeeeeeehhheeeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hlp B  21 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS 328
                                   |29        39        49    ||  57        67   ||   78        88        98       108       118       128       138       148       158       168       178       188       198       208  ||   224       234       244       254       264       274    || 285       295       305       315       325   
                                 27A                        53A|                71|                                                                                                                                       211|                                                          279|                                               
                                                             53B                 73                                                                                                                                        218                                                           281
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HLP)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MDH_HALMA | Q07841)
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.
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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 Related Entries

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        MDH_HALMA | Q07841: 1d3a 1o6z 2hlp 2j5k 2j5q 2j5r 2x0r 4jco

(-) Related Entries Specified in the PDB File

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