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Protein

Malate dehydrogenase [NADP], chloroplastic

Gene
N/A
Organism
Flaveria bidentis (Coastal plain yellowtops) (Ethulia bidentis)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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
Sitei88 – 881Activation of NADP-MDHBy similarity
Sitei93 – 931Activation of NADP-MDHBy similarity
Binding sitei198 – 1981SubstratePROSITE-ProRule annotation
Binding sitei204 – 2041SubstratePROSITE-ProRule annotation
Binding sitei211 – 2111NADPBy similarity
Binding sitei218 – 2181NADP1 Publication
Binding sitei237 – 2371SubstratePROSITE-ProRule annotation
Binding sitei268 – 2681SubstratePROSITE-ProRule annotation
Active sitei293 – 2931Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi117 – 1237NADP1 Publication
Nucleotide bindingi235 – 2373NADP1 Publication

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
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NADP

Names & Taxonomyi

Protein namesi
Recommended name:
Malate dehydrogenase [NADP], chloroplastic (EC:1.1.1.82)
Alternative name(s):
NADP-MDH
OrganismiFlaveria bidentis (Coastal plain yellowtops) (Ethulia bidentis)
Taxonomic identifieri4224 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridscampanulidsAsteralesAsteraceaeAsteroideaeHeliantheae allianceTageteaeFlaveria

Subcellular locationi

GO - Cellular componenti

  1. chloroplast Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6868ChloroplastAdd
BLAST
Chaini69 – 453385Malate dehydrogenase [NADP], chloroplasticPRO_0000018642Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi88 ↔ 93In oxidized inactive NAD-MDH
Disulfide bondi429 ↔ 441In oxidized inactive NAD-MDH

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1
453
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni90 – 934Combined sources
Beta strandi101 – 1033Combined sources
Beta strandi111 – 1166Combined sources
Turni117 – 1193Combined sources
Helixi121 – 13111Combined sources
Turni132 – 1365Combined sources
Beta strandi142 – 1476Combined sources
Helixi150 – 1523Combined sources
Helixi153 – 16412Combined sources
Turni165 – 1673Combined sources
Beta strandi171 – 1788Combined sources
Helixi180 – 1834Combined sources
Turni184 – 1863Combined sources
Beta strandi188 – 1925Combined sources
Helixi204 – 22522Combined sources
Beta strandi231 – 2344Combined sources
Beta strandi236 – 2383Combined sources
Helixi239 – 24810Combined sources
Helixi255 – 2573Combined sources
Beta strandi258 – 2603Combined sources
Helixi263 – 27715Combined sources
Beta strandi283 – 2853Combined sources
Beta strandi288 – 2914Combined sources
Beta strandi298 – 3003Combined sources
Helixi311 – 3133Combined sources
Helixi318 – 3236Combined sources
Helixi325 – 3295Combined sources
Helixi332 – 3387Combined sources
Helixi345 – 36016Combined sources
Beta strandi369 – 3746Combined sources
Beta strandi384 – 39310Combined sources
Beta strandi395 – 3984Combined sources
Helixi410 – 42920Combined sources
Turni430 – 4356Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CIVX-ray2.80A69-453[»]
ProteinModelPortaliP46489.
SMRiP46489. Positions 80-453.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP46489.

Family & Domainsi

Sequence similaritiesi

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

Keywords - Domaini

Transit peptide

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.

P46489-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVVKLSPWA NYSSSKSEIK SSSSSSSSKS SLSAYVINVS SSPRLSFYNP
60 70 80 90 100
YPRRLHHQRL SSPASIRCSV TSSDQIQAPL PAKQKPECFG VFCLTYDLKA
110 120 130 140 150
EEETKSWKKI INVAVSGAAG MISNHLLFKL ASGEVFGPDQ PISLKLLGSE
160 170 180 190 200
RSFAALEGVA MELEDSLYPL LRQVSIGIDP YEIFQDAEWA LLIGAKPRGP
210 220 230 240 250
GMERADLLDI NGQIFAEQGK ALNAVASPNV KVMVVGNPCN TNALICLKNA
260 270 280 290 300
PNIPPKNFHA LTRLDENRAK CQLALKAGVF YDKVSNVTIW GNHSTTQVPD
310 320 330 340 350
FLNAKIHGIP VTEVIRDRKW LEDEFTNMVQ TRGGVLIKKW GRSSAASTAV
360 370 380 390 400
SIVDAIRSLV TPTPEGDWFS TGVYTNGNPY GIAEDIVFSM PCRSKGDGDY
410 420 430 440 450
EFVKDVIFDD YLSKKIKKSE DELLAEKKCV AHLTGEGIAV CDLPEDTMLP

GEM
Length:453
Mass (Da):49,515
Last modified:November 1, 1995 - v1
Checksum:i7CD3A0F9F2A7B539
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L40958 mRNA. Translation: AAA63907.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L40958 mRNA. Translation: AAA63907.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CIVX-ray2.80A69-453[»]
ProteinModelPortaliP46489.
SMRiP46489. Positions 80-453.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP46489.

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]
ProtoNetiSearch...

Publicationsi

  1. Trevanion S.J., Ashton A.R.
    Submitted (APR-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Leaf.
  2. "Crystallization and preliminary crystallographic studies of chloroplast NADP-dependent malate dehydrogenase from Flaveria bidentis."
    Macpherson K.H., Ashton A.R., Carr P.D., Trevanion S.J., Verger D., Ollis D.L.
    Acta Crystallogr. D 54:654-656(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION.
  3. "Chloroplast NADP-malate dehydrogenase: structural basis of light-dependent regulation of activity by thiol oxidation and reduction."
    Carr P.D., Verger D., Ashton A.R., Ollis D.L.
    Structure 7:461-475(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
    Tissue: Leaf.

Entry informationi

Entry nameiMDHP_FLABI
AccessioniPrimary (citable) accession number: P46489
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: January 7, 2015
This is version 105 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

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 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.