Definition of L-glutamate catabolism

As rules and steps, or see full text

Rules

Overview: Glutamate is a single transamination reaction from 2-oxoglutarate (alpha-ketoglutarate), which is an intermediate in the TCA cycle. Amino acid transaminases are often non-specific, so glutamate catabolism could be considered trivial. However, many amino acid transaminases are 2-oxoglutarate dependent, so they cannot contribute to glutamate catabolism. And even if the amino group is transfered elsewhere, the ammonium group still needs to be liberated somehow. GapMind represents glutamate degradation using MetaCyc pathways L-glutamate degradation I (glutamate dehydrogenase, link), pathway II via aspartate ammonia-lyase (link), and pathway VI via glutamate mutase (link). Several other MetaCyc pathways are not included in GapMind. Pathway IV (via gamma-aminobutanoate, link) is not thought to occur in prokaryotes. Pathways V (via hydroxyglutarate, link) and XI (reductive Stickland reaction, link) combine glutamate dehydrogenase with reductive pathways; these are omitted because glutamate dehydrogenase alone suffices for catabolism under respiratory conditions. Pathways VII (to butanoate, link) and VIII (to propanoate, link) are similar to pathway VI but also describe the fermentation of the pyruvate. Pathway IX (via 4-aminobutanoate, link) does not yield net consumption of glutamate: the catabolism of 4-aminobutanoate relies on a transamination reaction that converts 2-oxoglutarate to glutamate.

• all:
  • glutamate-transport and gdhA
  • or glutamate-transport and aspA
  • or glutamate-transport, glmS, glmE, mal, fumD and mcl
  • Comment: GdhA is glutamate dehydrogenase (forming 2-oxoglutarate and ammonia). In pathway II, glutamate and oxaloacetate are transaminated to 2-oxoglutarate and aspartate, and the aspartate is cleaved to fumarate and ammonium by aspA. (The transamination reaction is not represented. Both oxaloacetate and fumarate are TCA cycle intermediates.) In pathway VI, the mutase glmSE converts glutamate to (2S,3S)-3-methylaspartate, the lyase mal forms 2-methylfumarate (mesaconate), the hydratase fumD forms (S)-2-methylmalate (citramalate), and a lyase forms acetate and pyruvate.
• glutamate-transport:
  • gltI, gltJ, gltK and gltL
  • or gltL, gluB, gluC and gluD
  • or bztA, bztB, bztC and gltL
  • or braC, braD, braE, braF and braG
  • or gltL and glnP
  • or peb1A, peb1B and gltL
  • or gtrA, gtrB and gtrC
  • or aapJ, aapQ, aapM and aapP
  • or gltS
  • or acaP
  • or gltP
  • or yveA
  • or gltS_Syn
  • or dmeA
  • Comment: Transporters were identified using query: transporter:glutamate:L-glutamate:glu

Steps

gltI: L-glutamate ABC transporter, substrate-binding component (GltI/AatJ)

• Curated sequence CH_002441: glutamate-aspartate periplasmic-binding protein. Glutamate/aspartate import solute-binding protein. YBEJ aka GltI aka B0655, component of Glutamate/aspartate porter. glutamate/aspartate ABC transporter periplasmic binding protein (EC 7.4.2.1). glutamate/aspartate ABC transporter periplasmic binding protein (EC 7.4.2.1)
• Curated sequence Q88NY2: PP1071, component of Acidic amino acid uptake porter, AatJMQP
• Curated sequence Pf1N1B4_771: ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component
• Curated sequence AO353_16290: ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, periplasmic substrate-binding component
• Curated sequence Q9I402: Probable binding protein component of ABC transporter, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida
• Ignore hits to PfGW456L13_4770 when looking for 'other' hits (ABC transporter for L-Asparagine and possibly other L-amino acids, periplasmic substrate-binding component)
• Total: 5 characterized proteins

gltJ: L-glutamate ABC transporter, permease component 1 (gltJ/aatQ)

• Curated sequence P0AER3: Glutamate/aspartate import permease protein GltJ. Glutamate/aspartate transport system permease protein GltJ aka B0654, component of Glutamate/aspartate porter. glutamate/aspartate ABC transporter membrane subunit GltJ (EC 7.4.2.1). glutamate/aspartate ABC transporter membrane subunit GltJ (EC 7.4.2.1)
• Curated sequence Q88NY3: PP1070, component of Acidic amino acid uptake porter, AatJMQP
• Curated sequence Pf1N1B4_772: ABC transporter for L-asparagine and L-glutamate, permease component 1
• Curated sequence AO353_16285: ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2
• Curated sequence Q9I403: Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida
• Ignore hits to PfGW456L13_4771 when looking for 'other' hits (ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1)
• Total: 5 characterized proteins

gltK: L-glutamate ABC transporter, permease component 1 (gltK/aatM)

• Curated sequence P0AER5: Glutamate/aspartate import permease protein GltK. Glutamate/aspartate transport system permease protein GltK aka B0653, component of Glutamate/aspartate porter. glutamate/aspartate ABC transporter membrane subunit GltK (EC 7.4.2.1). glutamate/aspartate ABC transporter membrane subunit GltK (EC 7.4.2.1)
• Curated sequence Q88NY4: PP1069, component of Acidic amino acid uptake porter, AatJMQP
• Curated sequence Pf1N1B4_773: ABC transporter for L-asparagine and L-glutamate, permease subunit 2
• Curated sequence AO353_16280: ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1
• Curated sequence Q9I404: Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida
• Ignore hits to PfGW456L13_4772 when looking for 'other' hits (ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2)
• Total: 5 characterized proteins

gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)

• Curated sequence A3ZI83: PEB1C, component of Uptake system for glutamate and aspartate
• Curated sequence P0AAG3: Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter. glutamate/aspartate ABC transporter ATP binding subunit (EC 7.4.2.1). glutamate/aspartate ABC transporter ATP binding subunit (EC 7.4.2.1)
• Curated sequence P48243: GluA aka CGL1950, component of Glutamate porter
• Curated sequence Q52666: BztD, component of Glutamate/glutamine/aspartate/asparagine porter
• Curated sequence Q88NY5: PP1068, component of Acidic amino acid uptake porter, AatJMQP
• Curated sequence Q9CES4: Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity
• Curated sequence Pf1N1B4_774: ABC transporter for L-asparagine and L-glutamate, ATPase component
• Curated sequence AO353_16275: ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component
• Curated sequence Q9I405: Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida
• Ignore hits to PfGW456L13_4773 when looking for 'other' hits (ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component)
• Ignore hits to SMc02121 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component)
• Ignore hits to Q52815 when looking for 'other' hits (AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux))
• Comment: SMc02121 is quite similar and is the ATPase component of a putative amino acid transporter, so it is ignored. Similarly for Q52815
• Total: 9 characterized proteins

gluB: L-glutamate ABC transporter, substrate-binding component GluB

• Curated sequence P48242: GluB aka CGL1951, component of Glutamate porter
• Comment: In Corynebacterium glutamicum, the ABC transporter is known as gluABCD. gluA is the ATPase component and is similar to gltL. gluB is the substrate-binding component and gluC/gluD are membrane components.
• Total: 1 characterized proteins

gluC: L-glutamate ABC transporter, permease component 1 (GluC)

• Curated sequence P48244: GluC aka CGL1952, component of Glutamate porter
• Total: 1 characterized proteins

gluD: L-glutamate ABC transporter, permease component 2 (GluD)

• Curated sequence P48245: GluD aka CGL1953, component of Glutamate porter
• Total: 1 characterized proteins

bztA: L-glutamate ABC transporter, substrate-binding component

• Curated sequence Q52663: BztA, component of Glutamate/glutamine/aspartate/asparagine porter
• Comment: In Rhodobacter capsulatus, the ABC transporter is known as bztABCD. BztD is the ATPase component and is similar to gltL
• Total: 1 characterized proteins

bztB: L-glutamate ABC transporter, permease component 1 (BztB)

• Curated sequence CH_011913: glutamate/glutamine/aspartate/asparagine transport system permease protein BztB. BztB, component of Glutamate/glutamine/aspartate/asparagine porter
• Total: 1 characterized proteins

bztC: L-glutamate ABC transporter, permease component 2 (BztC)

• Curated sequence Q52665: BztC, component of Glutamate/glutamine/aspartate/asparagine porter
• Total: 1 characterized proteins

braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC

• Curated sequence Q9L3M3: BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC
• Comment: In Rhizobium leguminosarum, a broad-specificity amino acid ABC transporter is known as braCDEFG. (A homologous system from Pseudomonas is thought to have a narrower substrate range.)
• Total: 1 characterized proteins

braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)

• UniProt sequence Q1MCU0: SubName: Full=Transmembrane component of a broad range amino acid ABC transporter {ECO:0000313|EMBL:CAK09240.1};
• Total: 1 characterized proteins

braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)

• UniProt sequence Q1MCU1: SubName: Full=Transmembrane component of a broad range amino acid ABC transporter {ECO:0000313|EMBL:CAK09239.1};
• Total: 1 characterized proteins

braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)

• UniProt sequence Q1MCU2: SubName: Full=ATP-binding component of a broad range amino acid ABC transporter {ECO:0000313|EMBL:CAK09238.1};
• Total: 1 characterized proteins

braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)

• UniProt sequence Q1MCU3: SubName: Full=ATP-binding component of a broad range amino acid ABC transporter {ECO:0000313|EMBL:CAK09237.1};
• Total: 1 characterized proteins

glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP

• Curated sequence Q9CES5: Glutamine ABC transporter permease and substrate binding protein protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity
• Comment: GlnQP from Lactococcus lactis, TC 3.A.1.3.25, has just two components: glnP has fused permease and substrate-binding domains, and glnQ is similar to gltL
• Total: 1 characterized proteins

peb1A: L-glutamate ABC transporter, substrate-binding component Peb1A

• Curated sequence CH_021449: major cell-binding factor. PEB1A, component of Uptake system for glutamate and aspartate
• Comment: Campylobacter has an ABC transporter with just 1 permease component (Peb1ABC). The ATPase component (peb1C) clusters with gltL
• Total: 1 characterized proteins

peb1B: L-glutamate ABC transporter, permease component Peb1B

• Curated sequence A1VZQ3: PEP1B, component of Uptake system for glutamate and aspartate
• Total: 1 characterized proteins

gtrA: tripartite L-glutamate:Na+ symporter, small membrane component GtrA

• Curated sequence P74225: GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter
• Comment: Synechocystis sp. PCC 6803 has a tripartite (DctMQP-like) glutamate transporter
• Total: 1 characterized proteins

gtrB: tripartite L-glutamate:Na+ symporter, large membrane component GtrB

• Curated sequence P74224: GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter
• Total: 1 characterized proteins

gtrC: tripartite L-glutamate:Na+ symporter, substrate-binding component GtrC

• Curated sequence P74223: GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter
• Total: 1 characterized proteins

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

• Curated sequence Q52812: AapJ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02118 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component)
• Total: 1 characterized proteins

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

• Curated sequence Q52813: AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02119 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1)
• Total: 1 characterized proteins

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

• Curated sequence Q52814: AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02120 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2)
• Total: 1 characterized proteins

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

• Curated sequence Q52815: AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux)
• Ignore hits to SMc02121 when looking for 'other' hits (ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component)
• Total: 1 characterized proteins

gltS: L-glutamate:Na+ symporter GltS

• Curated sequence P0AER8: Sodium/glutamate symporter; Glutamate permease. Glutamate:Na+ symporter (transports L- and D-glutamate, α-methylglutamate and homocysteate). Swapping the order of the two halves (repeat units) does not decrease activity. glutamate:sodium symporter
• Curated sequence P73275: Glutamate:Na+ symporter
• Curated sequence Q9HZ58: Probable L-glutamate/N-acetylglutamate uptake porter, GltS.  Involved in N-acetylglutamate catabolism as a carbon and nitrogen source
• Total: 3 characterized proteins

acaP: L-glutamate permease AcaP

• Curated sequence A2RL65: Aspartate/glutamate permease AcaP
• Curated sequence F2HJG8: Aspartate/Glutamate transporter of 488 aas and 12 TMSs, AcaP
• Ignore hits to P75835 when looking for 'other' hits (The GadC homologue)
• Total: 2 characterized proteins

gltP: L-glutamate:cation symporter GltP/GltT

• Curated sequence P21345: Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein. Glutamate/aspartate:H+ symporter, GltP or GltT; has 8 TMSs with 2 re-entrant loops as for GltPh (TC# 2.A.23.1.5). glutamate/aspartate : H⁺ symporter GltP
• Curated sequence P39817: Proton/glutamate-aspartate symporter; Proton/glutamate symport protein
• Curated sequence CH_088342: proton/sodium-glutamate symport protein GltT. Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein
• Curated sequence P24943: Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein. proton/sodium-glutamate symport protein GltT. Glutamate/aspartate:Na+ + H+ symporter
• UniProt sequence A1S570: SubName: Full=Sodium:dicarboxylate symporter {ECO:0000313|EMBL:ABL99526.1};
• UniProt sequence L0GT47: SubName: Full=Na+/H+ dicarboxylate symporter {ECO:0000313|EMBL:AGA88545.1};
• Ignore hits to O59010 when looking for 'other' hits (Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter. Archaeal aspartate transporter, Gltph (GltPh) (3-D structure known; 3V8F and 3V8G) (Boudker et al., 2007; Yernool et al., 2004). Cotransports aspartate with 2 Na+ (Ryan et al., 2009) or 3 Na+ (Groeneveld and Slotboom, 2010) or 1Na+ plus 1 H+ plus 1 K+)
• Total: 6 characterized proteins

yveA: L-glutamate:H+ symporter YveA

• Curated sequence O07002: Aspartate-proton symporter; L-aspartate transporter. The aspartate uptake permease, YveA
• Total: 1 characterized proteins

gltS_Syn: L-glutamate:Na+ symporter GltS_Syn

• Curated sequence B1XKD9: Glutamate:sodium symporter, GltS
• Total: 1 characterized proteins

dmeA: L-glutamate transporter DmeA

• Curated sequence Q31PG5: Possible transporter of polar amino acids including glutamate, glutamine and aspartate, DmeA. It complements a sepJ mutation in Anabaena (TC# 2.A.7.23.2), and SepJ complements a dmeA mutation. Alternatively, and less likely, it could be an activator of an ABC transporter catalyzing uptake of these amino acids
• Total: 1 characterized proteins

gdhA: glutamate dehydrogenase, NAD-dependent

• Curated proteins or TIGRFams with EC 1.4.1.2
• UniProt sequence G8AE86: RecName: Full=Glutamate dehydrogenase {ECO:0000256|ARBA:ARBA00012896}; EC=1.4.1.2 {ECO:0000256|ARBA:ARBA00012896};
• Ignore hits to items matching 1.4.1.3 when looking for 'other' hits
• Comment: The NADP dependent enzyme acts primarily in the reverse direction, so would not contribute to catabolism. EC 1.4.1.3 describes glutamate dehydrogenases that can use either NAD or NADP; these are ignored. AZOBR_RS00190 (G8AE86) is important for proline and glutamine catabolism, and both are catabolized via glutamate; this confirms it is a glutamate dehydrogenase.
• Total: 29 characterized proteins

aspA: L-aspartate ammonia-lyase

• Curated proteins or TIGRFams with EC 4.3.1.1
• Total: 1 HMMs and 4 characterized proteins

glmS: L-glutamate mutase, S component

• Curated sequence P80078: Glutamate mutase sigma subunit; Glutamate mutase S chain; Glutamate mutase small subunit; Methylaspartate mutase; EC 5.4.99.1. methylaspartate mutase (EC 5.4.99.1)
• Curated sequence Q05488: Glutamate mutase sigma subunit; Glutamate mutase S chain; Glutamate mutase small subunit; Methylaspartate mutase; EC 5.4.99.1. methylaspartate mutase (subunit 2/2) (EC 5.4.99.1)
• Curated sequence MONOMER-16253: glutamate mutase α subunit (EC 5.4.99.1)
• Total: 3 characterized proteins

glmE: L-glutamate mutase, E component

• Curated sequence P80077: Glutamate mutase epsilon subunit; Glutamate mutase E chain; Glutamate mutase large subunit; Methylaspartate mutase; EC 5.4.99.1. GlmE
• Curated sequence Q05509: Glutamate mutase epsilon subunit; Glutamate mutase E chain; Glutamate mutase large subunit; Methylaspartate mutase; EC 5.4.99.1. methylaspartate mutase (subunit 1/2) (EC 5.4.99.1)
• Curated sequence MONOMER-16254: glutamate mutase β subunit (EC 5.4.99.1)
• Total: 3 characterized proteins

mal: methylaspartate ammonia-lyase

• Curated proteins or TIGRFams with EC 4.3.1.2
• Total: 1 HMMs and 4 characterized proteins

fumD: (S)-2-methylmalate dehydratase (mesaconase)

• Curated proteins or TIGRFams with EC 4.2.1.34
• Ignore hits to items matching 4.2.1.2 when looking for 'other' hits
• Comment: An enzyme from Burkholderia xenovorans was shown to have a physiologically relevant mesaconase. Many fumarases (EC 4.2.1.2) may have this activity as well, so they are marked ignore.
• Total: 3 characterized proteins

mcl: (S)-citramalyl-CoA pyruvate-lyase

• Curated proteins or TIGRFams with EC 4.1.3.25
• Ignore hits to GFF3000 when looking for 'other' hits (Malyl-CoA lyase (EC 4.1.3.24))
• Ignore hits to B6E2X2 when looking for 'other' hits (L-malyl-CoA/beta-methylmalyl-CoA lyase; (3S)-malyl-CoA/beta-methylmalyl-CoA lyase; EC 4.1.3.24. malyl-CoA lyase subunit (EC 4.1.3.24))
• Comment: Although the citramalate lyase is described as a single reaction in MetaCyc, the enzyme database entry (EC 4.1.3.22) suggests that it is a two-step reaction: citramalate CoA-transferase (EC 2.8.3.11) and citramalyl-CoA lyase (EC 4.1.3.25). No citramalate CoA-transferase proteins have been linked to sequence, but citramalyl-CoA lyases are known, so only this step is included. Some (S-citramalyl-CoA lyases are very similar to malyl-CoA lyases, which are marked ignore.
• Total: 6 characterized proteins