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Protein

Malate synthase

Gene

aceB

Organism
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the glyoxylate cycle which synthesizes precursors for carbohydrates from C2 compounds such as acetate. Catalyzes the Claisen condensation between acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form the malyl-CoA intermediate that is subsequently hydrolyzed to produce malate and CoA.3 Publications

Catalytic activityi

Acetyl-CoA + H2O + glyoxylate = (S)-malate + CoA.1 Publication

Cofactori

Mg2+1 Publication

Kineticsi

AceB requires a high salt concentration for activity, the optimum being around 3.0 M KCl. Replacement of KCl by NaCl causes a decrease in activity (about 2-fold).

  1. KM=0.11 µM for glyoxylate (with 0.2 mM acetyl-CoA at pH 8 and 40 degrees Celsius)1 Publication
  2. KM=0.119 µM for acetyl-CoA (with 0.5 mM glyoxylate at pH 8 and 40 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is between 8 and 9.1 Publication

    Temperature dependencei

    Optimum temperature is between 45 and 65 degrees Celsius. The activity of the enzyme at 80 degrees Celsius is half of the maximum.1 Publication

    Pathwayi: glyoxylate cycle

    This protein is involved in step 2 of the subpathway that synthesizes (S)-malate from isocitrate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Isocitrate lyase (aceA)
    2. Malate synthase (aceB)
    This subpathway is part of the pathway glyoxylate cycle, which is itself part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes (S)-malate from isocitrate, the pathway glyoxylate cycle and in Carbohydrate metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi52Magnesium1 Publication1
    Binding sitei84Acetyl-CoA1 Publication1
    Binding sitei84Glyoxylate1 Publication1
    Metal bindingi158Magnesium1 Publication1
    Binding sitei158Glyoxylate1 Publication1
    Metal bindingi192Magnesium1 Publication1
    Binding sitei236Acetyl-CoA1
    Binding sitei259Acetyl-CoA; via carbonyl oxygen1
    Active sitei388Proton acceptorSequence analysis1

    GO - Molecular functioni

    • malate synthase activity Source: UniProtKB
    • metal ion binding Source: UniProtKB

    GO - Biological processi

    • glyoxylate cycle Source: UniProtKB
    • tricarboxylic acid cycle Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Glyoxylate bypass, Tricarboxylic acid cycle

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BRENDAi2.3.3.9. 2561.
    UniPathwayiUPA00703; UER00720.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Malate synthase (EC:2.3.3.9)
    Short name:
    MSH
    Gene namesi
    Name:aceB
    Synonyms:aceB1
    Ordered Locus Names:HVO_1983
    ORF Names:C498_05196
    OrganismiHaloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii)
    Taxonomic identifieri309800 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaHalobacteriaHaloferacalesHaloferacaceaeHaloferax
    Proteomesi
    • UP000011532 Componenti: Unassembled WGS sequence
    • UP000008243 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004295861 – 433Malate synthaseAdd BLAST433

    Interactioni

    Subunit structurei

    Homotrimer and homohexamer in equilibrium.3 Publications

    Protein-protein interaction databases

    STRINGi309800.HVO_1983.

    Structurei

    Secondary structure

    1433
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi13 – 19Combined sources7
    Beta strandi23 – 25Combined sources3
    Helixi29 – 36Combined sources8
    Helixi39 – 41Combined sources3
    Beta strandi44 – 51Combined sources8
    Helixi56 – 58Combined sources3
    Helixi59 – 73Combined sources15
    Helixi74 – 76Combined sources3
    Beta strandi78 – 81Combined sources4
    Helixi92 – 105Combined sources14
    Helixi108 – 110Combined sources3
    Helixi113 – 115Combined sources3
    Beta strandi118 – 121Combined sources4
    Helixi127 – 143Combined sources17
    Beta strandi151 – 157Combined sources7
    Helixi160 – 165Combined sources6
    Helixi166 – 168Combined sources3
    Helixi169 – 174Combined sources6
    Helixi180 – 182Combined sources3
    Beta strandi183 – 188Combined sources6
    Helixi190 – 197Combined sources8
    Helixi210 – 223Combined sources14
    Beta strandi226 – 229Combined sources4
    Helixi238 – 249Combined sources12
    Turni250 – 252Combined sources3
    Beta strandi255 – 258Combined sources4
    Helixi261 – 269Combined sources9
    Helixi329 – 334Combined sources6
    Helixi343 – 358Combined sources16
    Beta strandi364 – 369Combined sources6
    Beta strandi382 – 387Combined sources6
    Helixi389 – 395Combined sources7
    Helixi397 – 408Combined sources12
    Helixi410 – 412Combined sources3
    Helixi413 – 420Combined sources8
    Helixi422 – 428Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3OYXX-ray2.51A1-433[»]
    3OYZX-ray1.95A1-433[»]
    3PUGX-ray2.70A1-433[»]
    ProteinModelPortaliD4GTL2.
    SMRiD4GTL2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni16 – 17Acetyl-CoA binding1 Publication2
    Regioni191 – 192Glyoxylate binding1 Publication2

    Sequence similaritiesi

    Belongs to the HpcH/HpaI aldolase family.Curated

    Phylogenomic databases

    eggNOGiarCOG00760. Archaea.
    COG2301. LUCA.
    HOGENOMiHOG000094928.
    KOiK19282.
    OMAiEVDYTKD.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    InterProiIPR005000. Aldolase/citrate-lyase_domain.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PfamiPF03328. HpcH_HpaI. 1 hit.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    D4GTL2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTERRHDREF VRTFFTSPTA VEGEDDSAKM LRRAAGLRGM QAPDVWVPDN
    60 70 80 90 100
    EDATAPSMRD EGAENIVEVI SEQGAEFPGE IHPRMVWHRD SPETRYQGFQ
    110 120 130 140 150
    HMLDITDPER GAVEHIHGFV IPEVGGIDDW KKADEFFTIV EHEHGLDEGS
    160 170 180 190 200
    LAMSVIIESG EAELAMGDLR DEMGKPTNNL ERLFLLVDGE VDYTKDMRAM
    210 220 230 240 250
    TPTGELPAWP ELRHNTSRGA SAAGCVAVDG PYDDIRDVEG YRERMTDNQA
    260 270 280 290 300
    KGMLGIWSLT PGQVVEANTS PLPPKTGSWL LDADGEEVEL ASEDGVEAYD
    310 320 330 340 350
    GDRLSLEATD GGYELRVGGD ARELTADELR EELLGLTSYV PSMDDIVDSM
    360 370 380 390 400
    EEFEAAKEAG RGAIAMTQSA TLRIGGTEID IEKDRMWDEA TYQAAMTPIS
    410 420 430
    LFQDVYENRP DQHEELEERY GAGVVERAME VGL
    Length:433
    Mass (Da):48,018
    Last modified:May 18, 2010 - v1
    Checksum:i67AAD93EF9E576D9
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti326A → V in CAC48389 (PubMed:11513957).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ250923 Genomic DNA. Translation: CAC48389.1.
    CP001956 Genomic DNA. Translation: ADE04727.1.
    AOHU01000038 Genomic DNA. Translation: ELY34497.1.
    RefSeqiWP_004041864.1. NZ_AOHU01000038.1.

    Genome annotation databases

    EnsemblBacteriaiADE04727; ADE04727; HVO_1983.
    ELY34497; ELY34497; C498_05196.
    GeneIDi8925725.
    KEGGihvo:HVO_1983.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ250923 Genomic DNA. Translation: CAC48389.1.
    CP001956 Genomic DNA. Translation: ADE04727.1.
    AOHU01000038 Genomic DNA. Translation: ELY34497.1.
    RefSeqiWP_004041864.1. NZ_AOHU01000038.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3OYXX-ray2.51A1-433[»]
    3OYZX-ray1.95A1-433[»]
    3PUGX-ray2.70A1-433[»]
    ProteinModelPortaliD4GTL2.
    SMRiD4GTL2.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi309800.HVO_1983.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiADE04727; ADE04727; HVO_1983.
    ELY34497; ELY34497; C498_05196.
    GeneIDi8925725.
    KEGGihvo:HVO_1983.

    Phylogenomic databases

    eggNOGiarCOG00760. Archaea.
    COG2301. LUCA.
    HOGENOMiHOG000094928.
    KOiK19282.
    OMAiEVDYTKD.

    Enzyme and pathway databases

    UniPathwayiUPA00703; UER00720.
    BRENDAi2.3.3.9. 2561.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    InterProiIPR005000. Aldolase/citrate-lyase_domain.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PfamiPF03328. HpcH_HpaI. 1 hit.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiACEB_HALVD
    AccessioniPrimary (citable) accession number: D4GTL2
    Secondary accession number(s): Q977U4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 9, 2014
    Last sequence update: May 18, 2010
    Last modified: November 2, 2016
    This is version 41 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.