P36015

EV
Gene name
YKT6 (YKL196C)
Protein name
Synaptobrevin homolog YKT6
Names
Species
Escherichia coli (strain K12)
KEGG Pathway
sce:YKL196C
EC number
4.1.1.15: Carboxy-lyases
Protein Class

Descriptions

GadB, or glutamate decarboxylase, is an enzyme in Escherichia coli that helps the bacteria survive stomach acidity by converting glutamate to γ-aminobutyrate (GABA), consuming protons in the process. The N-terminal 14 residues of GadB are crucial for its function. Their deletion results in loss of cooperativity and sensitivity to chloride, affecting the enzyme’s activation. GadB can switch between active and inactive forms. At higher pH levels, it autoinhibits by forming a novel structure of the cofactor pyridoxal 5′-phosphate (aldamine), which involves a covalent bond with the enzyme’s histidine residue, leading to inactivation. This mechanism is significant for maintaining pH balance within the cell. Chloride ions, abundant in gastric secretions, act as allosteric activators of GadB, enhancing its decarboxylase activity and aiding in acid resistance.

Autoinhibitory domains (AIDs)

7-129 (Longin domain) EV

Target domain

140-200 (v-SNARE coiled-coil homology)

Relief mechanism

PTM

Assay

Structural analysis, Mutagenesis experiment

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

4 structures for P36015

Entry ID Method Resolution Chain Position Source
1H8M NMR - A 1-140 PDB
1IOU NMR - A 1-140 PDB
3BW6 X-ray 250 A A 1-140 PDB
AF-P36015-F1 Predicted AlphaFoldDB

No variants for P36015

Variant ID(s) Position Change Description Diseaes Association Provenance
No variants for P36015

No associated diseases with P36015

1 regional properties for P36015

Type Name Position InterPro Accession
binding_site Pyridoxal-phosphate binding site 269 - 290 IPR021115

Functions

Description
EC Number 4.1.1.15 Carboxy-lyases
Subcellular Localization
  • Cytoplasm
  • Membrane
  • Localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

8 GO annotations of cellular component

Name Definition
cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
endosome A vacuole to which materials ingested by endocytosis are delivered.
fungal-type vacuole A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
Golgi apparatus A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
membrane A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
SNARE complex A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.

2 GO annotations of molecular function

Name Definition
palmitoyltransferase activity Catalysis of the transfer of a palmitoyl (CH3-14-CO-) group to an acceptor molecule.
SNAP receptor activity Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.

9 GO annotations of biological process

Name Definition
amphisome-lysosome fusion The process in which amphisomes fuse with a vacuole (yeast) or lysosome (e.g. mammals and insects). In the case of yeast, inner membrane-bounded structures (autophagic bodies) appear in the vacuole. Fusion provides an acidic environment and digestive function to the interior of the amphisome.
endoplasmic reticulum to Golgi vesicle-mediated transport The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
Golgi to endosome transport The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes.
Golgi vesicle fusion to target membrane The joining of the lipid bilayer membrane around a Golgi transport vesicle to the target lipid bilayer membrane.
intra-Golgi vesicle-mediated transport The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
vacuole fusion, non-autophagic The fusion of two vacuole membranes to form a single vacuole.
vesicle fusion Fusion of the membrane of a transport vesicle with its target membrane.
vesicle fusion with Golgi apparatus The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.

8 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
Q3T000 YKT6 Synaptobrevin homolog YKT6 Bos taurus (Bovine) SS
O15498 YKT6 Synaptobrevin homolog YKT6 Homo sapiens (Human) SS
Q9CQW1 Ykt6 Synaptobrevin homolog YKT6 Mus musculus (Mouse) SS
Q5EGY4 Ykt6 Synaptobrevin homolog YKT6 Rattus norvegicus (Rat) EV
Q9LVM9 YKT62 VAMP-like protein YKT62 Arabidopsis thaliana (Mouse-ear cress) PR
Q9ZRD6 YKT61 VAMP-like protein YKT61 Arabidopsis thaliana (Mouse-ear cress) SS
Q6P816 ykt6 Synaptobrevin homolog YKT6 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) SS
Q7ZUN8 ykt6 Synaptobrevin homolog YKT6 Danio rerio (Zebrafish) (Brachydanio rerio) SS
10 20 30 40 50 60
MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL
70 80 90 100 110 120
ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG
130 140 150 160 170 180
TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI
190 200 210 220 230 240
PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM
250 260 270 280 290 300
HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV
310 320 330 340 350 360
FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL
370 380 390 400 410 420
GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV
430 440 450 460
MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT