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Protein

Malate dehydrogenase [NADP] 1, chloroplastic

Gene
N/A
Organism
Sorghum bicolor (Sorghum) (Sorghum vulgare)
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)DescriptionActionsGraphical viewLength
Sitei64Activation of NADP-MDH1
Sitei69Activation of NADP-MDH1
Binding sitei174SubstratePROSITE-ProRule annotation1
Binding sitei180SubstratePROSITE-ProRule annotation1
Binding sitei187NADPBy similarity1
Binding sitei194NADPBy similarity1
Binding sitei213SubstratePROSITE-ProRule annotation1
Binding sitei244SubstratePROSITE-ProRule annotation1
Active sitei269Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi93 – 99NADPBy similarity7
Nucleotide bindingi211 – 213NADPBy similarity3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NADP

Enzyme and pathway databases

BRENDAi1.1.1.82. 5768.
SABIO-RKP17606.

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 cladePanicoideaeAndropogonodaeAndropogoneaeSorghinaeSorghum

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 40ChloroplastBy similarityAdd BLAST40
ChainiPRO_000001864741 – 429Malate dehydrogenase [NADP] 1, chloroplasticAdd BLAST389

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi64 ↔ 69In oxidized inactive NAD-MDH
Disulfide bondi405 ↔ 417In oxidized inactive NAD-MDH

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP17606.

Expressioni

Gene expression databases

ExpressionAtlasiP17606. differential.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi4558.Sb07g023920.1.

Structurei

Secondary structure

1429
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi66 – 68Combined sources3
Beta strandi87 – 92Combined sources6
Turni93 – 95Combined sources3
Helixi97 – 107Combined sources11
Turni108 – 112Combined sources5
Beta strandi118 – 123Combined sources6
Helixi126 – 128Combined sources3
Helixi129 – 140Combined sources12
Beta strandi147 – 154Combined sources8
Helixi156 – 159Combined sources4
Turni160 – 162Combined sources3
Beta strandi164 – 168Combined sources5
Helixi180 – 201Combined sources22
Beta strandi207 – 210Combined sources4
Beta strandi212 – 214Combined sources3
Helixi215 – 224Combined sources10
Helixi231 – 233Combined sources3
Beta strandi234 – 236Combined sources3
Helixi239 – 252Combined sources14
Helixi257 – 259Combined sources3
Beta strandi264 – 267Combined sources4
Beta strandi274 – 276Combined sources3
Helixi287 – 289Combined sources3
Helixi294 – 306Combined sources13
Helixi308 – 315Combined sources8
Helixi321 – 336Combined sources16
Beta strandi345 – 350Combined sources6
Beta strandi360 – 369Combined sources10
Beta strandi372 – 374Combined sources3
Helixi386 – 405Combined sources20
Helixi407 – 410Combined sources4
Beta strandi412 – 414Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
7MDHX-ray2.40A/B/C/D55-429[»]
ProteinModelPortaliP17606.
SMRiP17606.
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

eggNOGiKOG1496. Eukaryota.
COG0039. LUCA.
HOGENOMiHOG000220953.
KOiK00051.
OMAiAFSQECI.
OrthoDBiEOG09360AEK.

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]
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. 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

« Hide

        10         20         30         40         50
MGLSTAYSPV GSHLAPAPLG HRRSAQLHRP RRALLATVRC SVDAAKQVQD
60 70 80 90 100
GVATAEAPAT RKDCFGVFCT TYDLKAEDKT KSWKKLVNIA VSGAAGMISN
110 120 130 140 150
HLLFKLASGE VFGQDQPIAL KLLGSERSFQ ALEGVAMELE DSLYPLLREV
160 170 180 190 200
SIGIDPYEVF EDVDWALLIG AKPRGPGMER AALLDINGQI FADQGKALNA
210 220 230 240 250
VASKNVKVLV VGNPCNTNAL ICLKNAPDIP AKNFHALTRL DENRAKCQLA
260 270 280 290 300
LKAGVFYDKV SNVTIWGNHS TTQVPDFLNA KIDGRPVKEV IKDTKWLEEE
310 320 330 340 350
FTITVQKRGG ALIQKWGRSS AASTAVSIAD AIKSLVTPTP EGDWFSTGVY
360 370 380 390 400
TTGNPYGIAE DIVFSMPCRS KGDGDYELAT DVSMDDFLWE RIKKSEAELL
410 420
AEKKCVAHLT GEGNAYCDVP EDTMLPGEV
Length:429
Mass (Da):46,455
Last modified:August 1, 1990 - v1
Checksum:i17D9E0A34A67F1FF
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti226 – 228APD → PPH in CAA37531 (PubMed:2209586).Curated3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

EnsemblPlantsiSb07g023920.1; Sb07g023920.1; Sb07g023920.
GeneIDi8057802.
GrameneiSb07g023920.1; Sb07g023920.1; Sb07g023920.
KEGGisbi:SORBI_07g023920.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31965 Genomic DNA. Translation: AAA34047.1.
X53453 mRNA. Translation: CAA37531.1.
PIRiJH0151.
S13588.
RefSeqiXP_002445670.1. XM_002445625.1.
UniGeneiSbi.76.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
7MDHX-ray2.40A/B/C/D55-429[»]
ProteinModelPortaliP17606.
SMRiP17606.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi4558.Sb07g023920.1.

Proteomic databases

PRIDEiP17606.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiSb07g023920.1; Sb07g023920.1; Sb07g023920.
GeneIDi8057802.
GrameneiSb07g023920.1; Sb07g023920.1; Sb07g023920.
KEGGisbi:SORBI_07g023920.

Phylogenomic databases

eggNOGiKOG1496. Eukaryota.
COG0039. LUCA.
HOGENOMiHOG000220953.
KOiK00051.
OMAiAFSQECI.
OrthoDBiEOG09360AEK.

Enzyme and pathway databases

BRENDAi1.1.1.82. 5768.
SABIO-RKP17606.

Miscellaneous databases

EvolutionaryTraceiP17606.

Gene expression databases

ExpressionAtlasiP17606. differential.

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]
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
TIGRFAMsiTIGR01757. Malate-DH_plant. 1 hit.
TIGR01759. MalateDH-SF1. 1 hit.
PROSITEiPS00068. MDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 132 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

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.