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(-) Description

Title :  R207S,R292S MUTANT OF MALATE DEHYDROGENASE FROM THE HALOPHILIC ARCHAEON HALOARCULA MARISMORTUI (HOLO FORM)
 
Authors :  A. Irimia, C. Ebel, F. M. D. Vellieux, S. B. Richard, L. W. Cosenza, G. Zaccai, D. Madern
Date :  17 Dec 09  (Deposition) - 29 Dec 09  (Release) - 29 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protein-Solvent Interaction, Haophilic, Ion-Binding, Oxidoreductase, Tricarboxylic Acid Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Irimia, C. Ebel, D. Madern, S. B. Richard, L. W. Cosenza, G. Zaccai, F. M. D. Vellieux
The Oligomeric States Of Haloarcula Marismortui Malate Dehydrogenase Are Modulated By Solvent Components As Shown By Crystallographic And Biochemical Studies
J. Mol. Biol. V. 326 859 2003
PubMed-ID: 12581646  |  Reference-DOI: 10.1016/S0022-2836(02)01450-X
(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: PET11A
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: HALOARCULA MARISMORTUI
    Organism Taxid: 2238

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2NA5Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:28 , GLY A:30 , THR A:31 , VAL A:32 , ASP A:53 , ILE A:54A , LYS A:55 , THR A:97 , ALA A:98 , GLY A:99 , ILE A:123 , THR A:138 , SER A:139 , ASN A:140 , PHE A:163 , LEU A:167 , HIS A:195 , HOH A:2048BINDING SITE FOR RESIDUE NAD A 607
02AC2SOFTWARELYS A:205 , ASP A:306 , ASP B:211BINDING SITE FOR RESIDUE CL A1001
03AC3SOFTWAREARG A:43 , ARG A:252 , ALA A:255 , HIS A:256 , GLU A:259BINDING SITE FOR RESIDUE CL A1004
04AC4SOFTWAREASP A:44 , ALA A:46 , ASP A:47BINDING SITE FOR RESIDUE NA A1007
05AC5SOFTWAREVAL B:27 , ALA B:29B , GLY B:30 , THR B:31 , VAL B:32 , ASP B:53 , THR B:97 , ALA B:98 , GLY B:99 , ARG B:102 , THR B:138 , SER B:139 , ASN B:140 , VAL B:142 , PHE B:163 , HIS B:195 , HOH B:2001 , HOH B:2018 , HOH B:2019 , HOH B:2071BINDING SITE FOR RESIDUE NAD B 608
06AC6SOFTWARETHR A:210B , ASP A:211 , LYS B:205 , ASP B:306BINDING SITE FOR RESIDUE CL B1002
07AC7SOFTWAREARG B:43 , ARG B:252 , ALA B:255 , HIS B:256 , GLU B:259BINDING SITE FOR RESIDUE CL B1005
08AC8SOFTWAREHOH A:2029 , LYS B:205 , SER B:207BINDING SITE FOR RESIDUE NA B1006
09AC9SOFTWAREILE B:40 , ALA B:41 , ASP B:44 , ILE B:45 , ALA B:46 , THR B:76BINDING SITE FOR RESIDUE NA B1008
10BC1SOFTWAREGLN B:80BINDING SITE FOR RESIDUE NA B1009
11BC2SOFTWAREASP B:143 , ASN B:146 , SER B:272 , ALA B:286BINDING SITE FOR RESIDUE NA B1010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X0R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X0R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X0R)

(-) Exons   (0, 0)

(no "Exon" information available for 2X0R)

(-) Sequences/Alignments

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: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 d2x0ra1 A:22-162 Malate dehydrogenase                                                                                                         d2x0ra2 A:163-330 Malate dehydrogenase                                                                                                                            SCOP domains
               CATH domains 2x0rA01 A:22-162 NAD(P)-binding Rossmann-like Domain                                                                                          2x0rA02 A:163-330 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.....ee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2x0r A   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVSVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVSLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50   |||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200      210A| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                      54A||                         81|                103|                       132A|                                                                          210A| ||                                                          280|              299|                             
                                  29B                       54B|                          84                 105                        132B                                                                           210B ||                                                           282               301                             
                                                             54C                                                                                                                                                          212|                                                                                                             
                                                                                                                                                                                                                           219                                                                                                             


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 d2x0rb1 B:22-162 Malate dehydrogenase                                                                                                         d2x0rb2 B:163-330 Malate dehydrogenase                                                                                                                            SCOP domains
               CATH domains 2x0rB01 B:22-162 NAD(P)-binding Rossmann-like Domain                                                                                          2x0rB02 B:163-330 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                       CATH domains
           Pfam domains (1) Ldh_1_N-2x0rB03 B:22-163                                                                                                                       -Ldh_1_C-2x0rB01 B:165-330                                                                                                                                       Pfam domains (1)
           Pfam domains (2) Ldh_1_N-2x0rB04 B:22-163                                                                                                                       -Ldh_1_C-2x0rB02 B:165-330                                                                                                                                       Pfam domains (2)
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh..hhh.eee.hhhhhhhhhhhhhhhh...hhh.ee..eee.....eee.....ee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhh..eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2x0r B   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVSVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVSLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50   |||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200      210A| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                      54A||                         81|                103|                       132A|                                                                          210A| ||                                                          280|              299|                             
                                  29B                       54B|                          84                 105                        132B                                                                           210B ||                                                           282               301                             
                                                             54C                                                                                                                                                          212|                                                                                                             
                                                                                                                                                                                                                           219
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: LDH_C (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric 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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MDH_HALMA | Q07841: 1d3a 1hlp 1o6z 2hlp 2j5k 2j5q 2j5r 4jco

(-) Related Entries Specified in the PDB File

1d3a CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
1hlp MALATE DEHYDROGENASE (HALOPHILIC) COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD)
1o6z 1.95 A RESOLUTION STRUCTURE OF (R207S, R292S) MUTANT OF MALATE DEHYDROGENASE FROM THE HALOPHILIC ARCHAEON HALOARCULA MARISMORTUI (HOLO FORM)
2hlp CRYSTAL STRUCTURE OF THE E267R MUTANT OF A HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
2j5k 2.0 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI (RADIATION DAMAGE SERIES)
2j5q 2.15 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI AFTER FIRST RADIATION BURN ( RADIATION DAMAGE SERIES)
2j5r 2.25 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI AFTER SECOND RADIATION BURN ( RADIATION DAMAGE SERIES)