NADP-dependent malic enzyme: Difference between revisions

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== Lysozyme ==
<StructureSection load='3wja' size='340' side='right' caption='The best structure for NADP-dependent malic enzyme shown: [[3wja]]' scene=''>
<StructureSection load='1swy' size='340' side='right' caption='Caption for this structure' scene=''>
Best example is PDB entry [[3wja]] and is shown in the viewer.<br>
Best example is 1swy<br>
==Catalytic Activity ==
Molecule Lysozyme, also known as Lysozyme, CP-7 lysin, Muramidase, Endolysin, 1,4-beta-N-acetylmuramidase, Lysis protein, CP-1 lysin, Lysozyme murein hydrolase, Protein gp17, Transglycosylase, Hevamine-A, Chitinase and L-alanyl-D-glutamate peptidase.
Oxaloacetate = pyruvate + CO(2).Data source: Uniprot [http://www.uniprot.org/uniprot/P48163 P48163]<br>
== Function ==
Or the decarboxylation of malate to pyruvate<ref>PMID:8187880</ref>.
lysozyme activity<br>
catalytic activity<br>
hydrolase activity<br>
hydrolase activity, acting on glycosyl bonds<br>
carbon-oxygen lyase activity, acting on polysaccharides<br>
lyase activity<br>
chitinase activity<br>
hydrolase activity, hydrolyzing O-glycosyl compounds<br>
sequence-specific DNA binding<br>


== Disease ==
{{#tree: id=OrganizedByTopic|openlevels=0|
*Item
**sub item
**Another sub-item
}}
== Relevance ==
== Structural highlights ==
== Biological process ==
== Biological process ==
Is involved in the following biological processes:<br>
Is involved in the following biological processes:<br>
cell wall macromolecule catabolic process<br>
malate metabolic process<br>
peptidoglycan catabolic process<br>
oxidation-reduction process<br>
metabolic process<br>
response to carbohydrate<br>
defense response to bacterium<br>
response to hormone<br>
cytolysis<br>
viral release from host cell<br>
carbohydrate metabolic process<br>
carbohydrate metabolic process<br>
chitin catabolic process<br>
protein tetramerization<br>
polysaccharide catabolic process<br>
regulation of NADP metabolic process<br>
cytolysis by virus of host cell<br>
NADP biosynthetic process<br>
cell wall organization<br>
small molecule metabolic process<br>
cellular lipid metabolic process<br>
== In structures ==
== In structures ==
Lysozyme is found in 595 PDB entries<br>
NADP-dependent malic enzyme is found in 3 PDB entries<br>
{{#tree:
*<b>Eukaryota</b> (3 PDB entries): <br>
*<b>Eukaryota<b> 16 PDB entries
**<b>Homo sapiens</b> (2 PDB entries): <br>
**<b>Homo sapiens</b> 1 PDB entries
***[[3wja]] <div class="pdb-prints 3wja"></div>
***[[4uis]]Title: The cryoEM structure of human gamma-Secretase complex
***Title: The crystal structure of human cytosolic NADP(+)-dependent malic enzyme in apo form
Experimental EM map [http://pdbe.org/emd-2974 emd-2974]. <br>
***2.548 A resolution
4.4 A resolution
***[http://www.ebi.ac.uk/pdbe/entry/search/index?organism_scientific_name:%22Homo%20sapiens%22&all_molecule_names:%22NADP-dependent%20malic%20enzyme%22&!chimera:y Search the PDB for NADP-dependent malic enzyme from Homo sapiens]
Other macromolecules also in this entry: GAMMA-SECRETASE, Nicastrin, Presenilin-1 NTF subunit, .
**<b>Columba livia</b> (1 PDB entries): <br>
**<b>Hevea brasiliensis</b> 7 PDB entries
***[[1gq2]] <div class="pdb-prints 1gq2"></div>
***[[1kqy]]Title: Hevamine Mutant D125A/E127A/Y183F in Complex with Penta-NAG
***Title: MALIC ENZYME FROM PIGEON LIVER
1.92 A resolution
***2.5 A resolution
 
== Alternative names for NADP-dependent malic enzyme ==
**<b>Meretrix lusoria</b> 3 PDB entries
Molecule '''NADP-dependent malic enzyme''', also known as '''NADP-ME''', '''NADP-dependent malic enzyme''' and '''Malic enzyme 1'''.
***[[4pj2]]Title: Crystal structure of Aeromonas hydrophila PliI in complex with Meretrix lusoria lysozyme
1.24 A resolution
Other macromolecules also in this entry: Putative exported protein, .
**<b>Antheraea mylitta</b> 1 PDB entries
***[[1iiz]]Title: Crystal Structure of the Induced Antibacterial Protein from Tasar Silkworm, Antheraea mylitta
2.4 A resolution  
 
**<b>Ruditapes philippinarum</b> 1 PDB entries
***[[2dqa]]Title: Crystal Structure of Tapes japonica Lysozyme
1.6 A resolution
 
**<b>Mus musculus</b> 1 PDB entries
***[[1iak]]Title: HISTOCOMPATIBILITY ANTIGEN I-AK
1.9 A resolution
Other macromolecules also in this entry: H-2 class II histocompatibility antigen, A-K beta chain, H-2 class II histocompatibility antigen, A-K alpha chain.
**<b>Bombyx mori</b> 2 PDB entries
***[[1gd6]]Title: STRUCTURE OF THE BOMBYX MORI LYSOZYME
2.5 A resolution
 
*<b>Viruses<b> 578 PDB entries
**<b>Enterobacteria phage P22</b> 2 PDB entries
***[[2anv]]Title: crystal structure of P22 lysozyme mutant L86M
1.04 A resolution
 
**<b>Enterobacteria phage P21</b> 2 PDB entries
***[[3hdf]]Title: Crystal structure of truncated endolysin R21 from phage 21
1.7 A resolution
 
**<b>Enterobacteria phage T4</b> 561 PDB entries
***[[1swy]]Title: Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure Determination
1.06 A resolution  
 
**<b>Escherichia phage T5</b> 1 PDB entries
***[[2mxz]]Title: Bacteriophage T5 l-alanoyl-d-glutamate peptidase comlpex with Zn2+ (Endo T5-ZN2+)
N/A A resolution


**<b>Enterobacteria phage lambda</b> 3 PDB entries
== 3D Structures of NADP-dependent malic enzyme ==
***[[1am7]]Title: Lysozyme from bacteriophage lambda
2.3 A resolution


**<b>Streptococcus phage CP-7</b> 1 PDB entries
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
***[[4cvd]]Title: Crystal structure of the central repeat of cell wall binding module of Cpl7
1.666 A resolution


**<b>Enterobacteria phage P1</b> 2 PDB entries
[[3wja]], [[2aw5]] – hME - human<br />
***[[1xju]]Title: Crystal structure of secreted inactive form of P1 phage endolysin Lyz
[[7x11]], [[7x12]] – hME1 + NADP<br />
1.07 A resolution
[[8e76]], [[8eyn]] – hME3<br />
[[8e78]], [[8e8o]], [[8eyo]] – hME3 + NADP<br />
[[1gq2]] – ME + NADP - pigeon<br />
[[5ou5]] – maME 62-636 - maize<br />
[[9e6m]] – maME 62-636 (mutant) + pyruvate <br />
[[9ks0]] – EcME PTA domain 429-759 – ''Eschericia coli''<br />
[[8jzo]], [[9krw]] – EcME – Cryo EM<br />
[[9m2i]] – EcME ME domain 1-440 – Cryo EM<br />
[[9krt]] – EcME + NADP – Cryo EM<br />
[[9m35]] – EcME ME domain + NADP – Cryo EM<br />
[[9l4n]] – EcME + acetyl CoA + NADP - Cryo EM<br />
[[9kru]] – BbME + NADP – ''Bdellovibrio bacteriovorus'' - Cryo EM<br />
[[9krv]] – BbME + acetyl CoA + NADP - Cryo EM<br />


**<b>Streptococcus phage Cp-1</b> 6 PDB entries
***[[2j8g]]Title: Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant in complex with a tetrasaccharide- pentapeptide)
1.69 A resolution


*<b>Bacteria<b> 1 PDB entries
== References ==
**<b>Enterobacteria phage T4</b> 1 PDB entries
<references/>
***[[2qb0]]Title: Structure of the 2TEL crystallization module fused to T4 lysozyme with an Ala-Gly-Pro linker.
[[Category:Topic Page]][[Category:PDBe]]
2.56 A resolution
Other macromolecules also in this entry: Transcription factor ETV6, .
**<b>Escherichia coli</b> 1 PDB entries
***[[2qb0]]Title: Structure of the 2TEL crystallization module fused to T4 lysozyme with an Ala-Gly-Pro linker.
2.56 A resolution
Other macromolecules also in this entry: Transcription factor ETV6, .
}}

Latest revision as of 10:30, 24 March 2026

<StructureSection load='3wja' size='340' side='right' caption='The best structure for NADP-dependent malic enzyme shown: 3wja' scene=> Best example is PDB entry 3wja and is shown in the viewer.

Catalytic Activity

Oxaloacetate = pyruvate + CO(2).Data source: Uniprot P48163
Or the decarboxylation of malate to pyruvate[1].

Biological process

Is involved in the following biological processes:
malate metabolic process
oxidation-reduction process
response to carbohydrate
response to hormone
carbohydrate metabolic process
protein tetramerization
regulation of NADP metabolic process
NADP biosynthetic process
small molecule metabolic process
cellular lipid metabolic process

In structures

NADP-dependent malic enzyme is found in 3 PDB entries

Alternative names for NADP-dependent malic enzyme

Molecule NADP-dependent malic enzyme, also known as NADP-ME, NADP-dependent malic enzyme and Malic enzyme 1.

3D Structures of NADP-dependent malic enzyme

Updated on 24-March-2026


3wja, 2aw5 – hME - human
7x11, 7x12 – hME1 + NADP
8e76, 8eyn – hME3
8e78, 8e8o, 8eyo – hME3 + NADP
1gq2 – ME + NADP - pigeon
5ou5 – maME 62-636 - maize
9e6m – maME 62-636 (mutant) + pyruvate
9ks0 – EcME PTA domain 429-759 – Eschericia coli
8jzo, 9krw – EcME – Cryo EM
9m2i – EcME ME domain 1-440 – Cryo EM
9krt – EcME + NADP – Cryo EM
9m35 – EcME ME domain + NADP – Cryo EM
9l4n – EcME + acetyl CoA + NADP - Cryo EM
9kru – BbME + NADP – Bdellovibrio bacteriovorus - Cryo EM
9krv – BbME + acetyl CoA + NADP - Cryo EM


References

  1. ↑ Loeber G, Dworkin MB, Infante A, Ahorn H. Characterization of cytosolic malic enzyme in human tumor cells. FEBS Lett. 1994 May 16;344(2-3):181-6. PMID:8187880

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PDBe, Michal Harel, Jaime Prilusky

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