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P17606

- MDHP1_SORBI

UniProt

P17606 - MDHP1_SORBI

Protein

Malate dehydrogenase [NADP] 1, chloroplastic

Gene
N/A
Organism
Sorghum bicolor (Sorghum) (Sorghum vulgare)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 1 (01 Aug 1990)
      Previous versions | rss
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    Functioni

    The chloroplastic, NADP-dependent form is essential for the photosynthesis C4 cycle, which allows plants to circumvent the problem of photorespiration. In C4 plants, NADP-MDH activity acts to convert oxaloacetate to malate in chloroplasts of mesophyll cells for transport to the bundle sheath cells.

    Catalytic activityi

    (S)-malate + NADP+ = oxaloacetate + NADPH.

    Enzyme regulationi

    Chloroplast NADP-MDH is activated upon illumination. In order to be enzymatically active, disulfide bridges on the protein must be reduced by thioredoxin which receives electrons from ferredoxin and the electron transport system of photosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei64 – 641Activation of NADP-MDH
    Sitei69 – 691Activation of NADP-MDH
    Binding sitei174 – 1741SubstratePROSITE-ProRule annotation
    Binding sitei180 – 1801SubstratePROSITE-ProRule annotation
    Binding sitei187 – 1871NADPBy similarity
    Binding sitei194 – 1941NADPBy similarity
    Binding sitei213 – 2131SubstratePROSITE-ProRule annotation
    Binding sitei244 – 2441SubstratePROSITE-ProRule annotation
    Active sitei269 – 2691Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi93 – 997NADPBy similarity
    Nucleotide bindingi211 – 2133NADPBy similarity

    GO - Molecular functioni

    1. malate dehydrogenase (NADP+) activity Source: UniProtKB-EC

    GO - Biological processi

    1. carbohydrate metabolic process Source: InterPro
    2. malate metabolic process Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BRENDAi1.1.1.82. 5768.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Malate dehydrogenase [NADP] 1, chloroplastic (EC:1.1.1.82)
    Alternative name(s):
    NADP-MDH-1
    OrganismiSorghum bicolor (Sorghum) (Sorghum vulgare)
    Taxonomic identifieri4558 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaePACMAD cladePanicoideaeAndropogoneaeSorghum

    Organism-specific databases

    GrameneiP17606.

    Subcellular locationi

    GO - Cellular componenti

    1. chloroplast Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 4040ChloroplastBy similarityAdd
    BLAST
    Chaini41 – 429389Malate dehydrogenase [NADP] 1, chloroplasticPRO_0000018647Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi64 ↔ 69In oxidized inactive NAD-MDH
    Disulfide bondi405 ↔ 417In oxidized inactive NAD-MDH

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1
    429
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi66 – 683
    Beta strandi87 – 926
    Turni93 – 953
    Helixi97 – 10711
    Turni108 – 1125
    Beta strandi118 – 1236
    Helixi126 – 1283
    Helixi129 – 14012
    Beta strandi147 – 1548
    Helixi156 – 1594
    Turni160 – 1623
    Beta strandi164 – 1685
    Helixi180 – 20122
    Beta strandi207 – 2104
    Beta strandi212 – 2143
    Helixi215 – 22410
    Helixi231 – 2333
    Beta strandi234 – 2363
    Helixi239 – 25214
    Helixi257 – 2593
    Beta strandi264 – 2674
    Beta strandi274 – 2763
    Helixi287 – 2893
    Helixi294 – 30613
    Helixi308 – 3158
    Helixi321 – 33616
    Beta strandi345 – 3506
    Beta strandi360 – 36910
    Beta strandi372 – 3743
    Helixi386 – 40520
    Helixi407 – 4104
    Beta strandi412 – 4143

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    7MDHX-ray2.40A/B/C/D55-429[»]
    ProteinModelPortaliP17606.
    SMRiP17606. Positions 61-426.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17606.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the LDH/MDH superfamily. MDH type 2 family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0039.
    HOGENOMiHOG000220953.
    KOiK00051.
    OMAiFPDYRHA.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.110.10. 1 hit.
    InterProiIPR022383. Lactate/malate_DH_C.
    IPR001236. Lactate/malate_DH_N.
    IPR015955. Lactate_DH/Glyco_Ohase_4_C.
    IPR001252. Malate_DH_AS.
    IPR011273. Malate_DH_NADP-dep_pln.
    IPR010945. Malate_DH_type2.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR23382. PTHR23382. 1 hit.
    PfamiPF02866. Ldh_1_C. 1 hit.
    PF00056. Ldh_1_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF56327. SSF56327. 1 hit.
    TIGRFAMsiTIGR01757. Malate-DH_plant. 1 hit.
    TIGR01759. MalateDH-SF1. 1 hit.
    PROSITEiPS00068. MDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P17606-1 [UniParc]FASTAAdd to Basket

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    MGLSTAYSPV GSHLAPAPLG HRRSAQLHRP RRALLATVRC SVDAAKQVQD    50
    GVATAEAPAT RKDCFGVFCT TYDLKAEDKT KSWKKLVNIA VSGAAGMISN 100
    HLLFKLASGE VFGQDQPIAL KLLGSERSFQ ALEGVAMELE DSLYPLLREV 150
    SIGIDPYEVF EDVDWALLIG AKPRGPGMER AALLDINGQI FADQGKALNA 200
    VASKNVKVLV VGNPCNTNAL ICLKNAPDIP AKNFHALTRL DENRAKCQLA 250
    LKAGVFYDKV SNVTIWGNHS TTQVPDFLNA KIDGRPVKEV IKDTKWLEEE 300
    FTITVQKRGG ALIQKWGRSS AASTAVSIAD AIKSLVTPTP EGDWFSTGVY 350
    TTGNPYGIAE DIVFSMPCRS KGDGDYELAT DVSMDDFLWE RIKKSEAELL 400
    AEKKCVAHLT GEGNAYCDVP EDTMLPGEV 429
    Length:429
    Mass (Da):46,455
    Last modified:August 1, 1990 - v1
    Checksum:i17D9E0A34A67F1FF
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti226 – 2283APD → PPH in CAA37531. (PubMed:2209586)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M31965 Genomic DNA. Translation: AAA34047.1.
    X53453 mRNA. Translation: CAA37531.1.
    PIRiJH0151.
    S13588.
    RefSeqiXP_002445670.1. XM_002445625.1.
    UniGeneiSbi.76.

    Genome annotation databases

    GeneIDi8057802.
    KEGGisbi:SORBI_07g023920.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M31965 Genomic DNA. Translation: AAA34047.1 .
    X53453 mRNA. Translation: CAA37531.1 .
    PIRi JH0151.
    S13588.
    RefSeqi XP_002445670.1. XM_002445625.1.
    UniGenei Sbi.76.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    7MDH X-ray 2.40 A/B/C/D 55-429 [» ]
    ProteinModelPortali P17606.
    SMRi P17606. Positions 61-426.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 8057802.
    KEGGi sbi:SORBI_07g023920.

    Organism-specific databases

    Gramenei P17606.

    Phylogenomic databases

    eggNOGi COG0039.
    HOGENOMi HOG000220953.
    KOi K00051.
    OMAi FPDYRHA.

    Enzyme and pathway databases

    BRENDAi 1.1.1.82. 5768.

    Miscellaneous databases

    EvolutionaryTracei P17606.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    3.90.110.10. 1 hit.
    InterProi IPR022383. Lactate/malate_DH_C.
    IPR001236. Lactate/malate_DH_N.
    IPR015955. Lactate_DH/Glyco_Ohase_4_C.
    IPR001252. Malate_DH_AS.
    IPR011273. Malate_DH_NADP-dep_pln.
    IPR010945. Malate_DH_type2.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    PANTHERi PTHR23382. PTHR23382. 1 hit.
    Pfami PF02866. Ldh_1_C. 1 hit.
    PF00056. Ldh_1_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56327. SSF56327. 1 hit.
    TIGRFAMsi TIGR01757. Malate-DH_plant. 1 hit.
    TIGR01759. MalateDH-SF1. 1 hit.
    PROSITEi PS00068. MDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Structure and characterization of the Sorghum vulgare gene encoding NADP-malate dehydrogenase."
      Luchetta P., Cretin C., Gadal P.
      Gene 89:171-177(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: cv. INRA 450.
      Tissue: Leaf.
    2. "Primary structure of sorghum malate dehydrogenase (NADP) deduced from cDNA sequence. Homology with malate dehydrogenase (NAD)."
      Cretin C., Luchetta P., Joly C., Decottignies P., Lepiniec L., Gadal P., Sallantin M., Huet J.-C., Pernollet J.-C.
      Eur. J. Biochem. 192:299-303(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: cv. Tamaran FNK 140.
      Tissue: Leaf.
    3. "Structural basis for light activation of a chloroplast enzyme: the structure of sorghum NADP-malate dehydrogenase in its oxidized form."
      Johansson K., Ramaswamy S., Saarinen M., Lemaire-Chamley M., Issakidis-Bourguet E., Miginiac-Maslow M., Eklund H.
      Biochemistry 38:4319-4326(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), SUBUNIT.

    Entry informationi

    Entry nameiMDHP1_SORBI
    AccessioniPrimary (citable) accession number: P17606
    Secondary accession number(s): P19796
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: August 1, 1990
    Last modified: October 1, 2014
    This is version 119 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

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

    External Data

    Dasty 3