Definition of D-mannose catabolism

As rules and steps, or see full text

Rules

Overview: Mannose utilization in GapMind is based on MetaCyc pathways D-mannose degradation I via a PTS system (link), pathway II via mannose kinase (link), or conversion to fructose by mannose isomerase.

• all:
  • mannose-PTS and manA
  • or mannose-transport, mannokinase and manA
  • or mannose-transport, man-isomerase and scrK
  • Comment: In pathway I, after uptake and phosphorlation by a PTS system, mannose-6-phosphate isomerase (manA) produces fructose-6-phosphate, which is a central metabolic intermediate. In pathway II, after uptake, mannose kinase is followed by isomerization to fructose 6-phosphate. Or, D-mannose isomerase yields fructose, which can be metabolized by fructokinase (scrK).
• mannose-transport:
  • glcS, glcT, glcU and glcV
  • or TT_C0211, TT_C0327, TT_C0326 and TT_C0328
  • or TM1746, TM1747, TM1748, TM1749 and TM1750
  • or frcA, frcB and frcC
  • or HSERO_RS03635, HSERO_RS03640 and HSERO_RS03645
  • or STP6
  • or gluP
  • or glcP
  • or MST1
  • or manMFS
  • Comment: Transporters and PTS systems were identified using query: transporter:mannose:D-mannose:D-mannopyranose:CPD-13559:CPD-12601
• mannose-PTS:
  • manX, manY and manZ
  • or manP
  • Comment: PTS systems form D-mannose 6-phosphate

Steps

manX: mannose PTS system, EII-AB component ManX/ManL

• Curated sequence CH_088329: PTS system mannose-specific EIIAB component; EC 2.7.1.-; EC 2.7.1.69. PTS system mannose-specific EIIAB component; EIIAB-Man; EIII-Man; EC 2.7.1.191. PTNA aka MANX aka PTSL aka GPTB aka B1817, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose. mannose-specific PTS enzyme IIAB component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IIAB component
• Curated sequence D2BKY7: Mannose-specificPTS system, IIAB component, component of Mannose enzyme II complex, IIAB, IIC, IID. IIC/IID serve allows entry of some bacteriocins including pediocin (class IIa) and lactococcin A (class IIc) (Kjos et al., 2011). Transports and phosphorylates Glucose, Mannose and Glucosamine
• Curated sequence E1UCI0: PTS system, mannose-specific, IIAB component, component of The primary glucose /mannose uptake transporter, ManLMN
• Ignore hits to Q5M5W6 when looking for 'other' hits (ManL, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN)
• Ignore hits to Q9S4L5 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191))
• Ignore hits to Q04GK1 when looking for 'other' hits (Phosphotransferase system, mannose/fructose-specific component IIA, component of The hexose (glucose and fructose demonstrated) PTS uptake system)
• Ignore hits to Q2QKM4 when looking for 'other' hits (ManL aka EIIAB, component of Glucose porter, ManLMN)
• Comment: E. coli has manXYZ, where manX has EII-AB, manY has EII-C, and manZ has EII-D. (ManZ is listed twice with slightly different sequence lengths). Similar systems are known in Lactococcus lactis, Listeria monocytogenes, and Streptococcus thermophilus. However, the S. thermophilus system seems not to be active due to a defective IIC domain (PMID:12957931), so those proteins are marked ignore. L. monocytogenes also has a PTS-like regulatory system, mpoABCD, which is not included. (It is reported to act as a glucose transporter, but slowly; not clear if it transports mannose.) There's also a paper about manLMN from Streptococcus salivarius, but I don't think it is actually characterized, so ignore. Closely related to some systems with unclear specificity, ignore those.
• Total: 3 characterized proteins

manY: mannose PTS system, EII-C component ManY/ManM

• Curated sequence CH_088330: mannose permease IIC component. PTS system mannose-specific EIIC component; EII-P-Man; EIIC-Man; Mannose permease IIC component. PTNC aka MANY aka PTSP aka PEL aka B1818, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose. mannose-specific PTS enzyme IIC component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IIC component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193)
• Curated sequence D2BKY8: Mannose-specific PTS system, IIC component, component of Mannose enzyme II complex, IIAB, IIC, IID. IIC/IID serve allows entry of some bacteriocins including pediocin (class IIa) and lactococcin A (class IIc) (Kjos et al., 2011). Transports and phosphorylates Glucose, Mannose and Glucosamine
• Curated sequence E1UCI1: PTS system, mannose/fructose/sorbose family, IIC component, component of The primary glucose /mannose uptake transporter, ManLMN
• Ignore hits to Q5M5W7 when looking for 'other' hits (ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN)
• Ignore hits to Q8Y8W0 when looking for 'other' hits (Lmo0782 protein, component of Constitutively synthesized sensor, MpoABCD, controlling man operon (see TC# 4.A.6.1.15) expression by interacting with and phosphorylating ManR, the transcriptional regulator of the man operon)
• Ignore hits to Q04GK0 when looking for 'other' hits (Mannose-specific PTS system component IIC, component of The hexose (glucose and fructose demonstrated) PTS uptake system)
• Ignore hits to Q2QKM3 when looking for 'other' hits (ManM aka EIIC, component of Glucose porter, ManLMN)
• Total: 3 characterized proteins

manZ: mannose PTS system, EII-D component ManZ/ManN

• Curated sequence P69805: PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component. mannose-specific PTS enzyme IID component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IID component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193)
• Curated sequence D2BKY9: Mannose-specific PTS system, IID component, component of Mannose enzyme II complex, IIAB, IIC, IID. IIC/IID serve allows entry of some bacteriocins including pediocin (class IIa) and lactococcin A (class IIc) (Kjos et al., 2011). Transports and phosphorylates Glucose, Mannose and Glucosamine
• Curated sequence E1UCI2: PTS system, mannose/fructose/sorbose family, IID component, component of The primary glucose /mannose uptake transporter, ManLMN
• Curated sequence P69805: PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose
• Ignore hits to Q5M5W8 when looking for 'other' hits (ManN, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN)
• Ignore hits to Q04GJ9 when looking for 'other' hits (PTS system IID component, Man family, component of The hexose (glucose and fructose demonstrated) PTS uptake system)
• Ignore hits to Q2QKM2 when looking for 'other' hits (ManN aka EIID, component of Glucose porter, ManLMN)
• Ignore hits to Q5IRC0 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191))
• Ignore hits to Q8Y8W1 when looking for 'other' hits (Lmo0781 protein, component of Constitutively synthesized sensor, MpoABCD, controlling man operon (see TC# 4.A.6.1.15) expression by interacting with and phosphorylating ManR, the transcriptional regulator of the man operon)
• Total: 4 characterized proteins

manP: mannose PTS system, EII-CBA components

• Curated sequence O31645: protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191). PTS system mannose-specific EIIBCA component; EIIBCA-Man; EII-Man; EC 2.7.1.191. The mannose porter (ManP) (37% identical to 4.A.2.1.1). It is encoded in an operon with 3 genes:
• Comment: B. subtilis has a combined EII-BCA PTS system
• Total: 1 characterized proteins

glcS: mannose ABC transporter, substrate-binding component GlcS

• Curated sequence Q97UZ1: Glucose-binding protein GlcS; GBP. GlcS, component of Glucose, mannose, galactose porter
• Comment: The Saccharolobus solfataricus system (4 components)
• Total: 1 characterized proteins

glcT: mannose ABC transporter, permease component 1 (GlcT)

• Curated sequence Q97UZ0: GlcT, component of Glucose, mannose, galactose porter
• Total: 1 characterized proteins

glcU: mannose ABC transporter, permease component 2 (GlcU)

• Curated sequence Q97UY9: GlcU, component of Glucose, mannose, galactose porter
• Total: 1 characterized proteins

glcV: mannose ABC transporter, ATPase component GlcV

• Curated sequence Q97UY8: monosaccharide-transporting ATPase (EC 3.6.3.17). Glucose import ATP-binding protein GlcV; EC 7.5.2.-. GlcV, component of Glucose, mannose, galactose porter
• Total: 1 characterized proteins

TT_C0211: mannose ABC transporter, ATPase component MalK1

• Curated sequence Q72L52: Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose
• Comment: The Thermus thermophilus system (4 components)
• Total: 1 characterized proteins

TT_C0327: mannose ABC transporter, permease component 1

• Curated sequence Q72KX3: Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
• Total: 1 characterized proteins

TT_C0326: mannose ABC transporter, permease component 2

• Curated sequence Q72KX4: Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
• Total: 1 characterized proteins

TT_C0328: mannose ABC transporter, substrate-binding component

• Curated sequence Q72KX2: Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
• Total: 1 characterized proteins

TM1746: mannose ABC transporter, substrate-binding component

• Curated sequence Q9X268: TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR
• Comment: The Thermotoga maritima system (5 components)
• Total: 1 characterized proteins

TM1747: mannose ABC transporter, permease component 1

• Curated sequence Q9X269: TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR
• Total: 1 characterized proteins

TM1748: mannose ABC transporter, permease component 2

• Curated sequence Q9X270: TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR
• Total: 1 characterized proteins

TM1749: mannose ABC transporter, ATPase component 1

• Curated sequence Q9X271: TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR
• Total: 1 characterized proteins

TM1750: mannose ABC transporter, ATPase component 2

• Curated sequence Q9X272: TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR
• Total: 1 characterized proteins

frcA: mannose ABC transporter, ATPase component FrcA

• Curated sequence Q9F9B0: Fructose import ATP-binding protein FrcA; EC 7.5.2.-. FrcA, component of Fructose/mannose/ribose porter
• Comment: The Ensifer meliloti system (3 components)
• Total: 1 characterized proteins

frcB: mannose ABC transporter, substrate-binding component FrcB

• Curated sequence Q9F9B2: Fructose import binding protein FrcB. FrcB, component of Fructose/mannose/ribose porter
• Total: 1 characterized proteins

frcC: mannose ABC transporter, permease component FrcC

• Curated sequence Q9F9B1: Fructose import permease protein FrcC. FrcC, component of Fructose/mannose/ribose porter
• Total: 1 characterized proteins

HSERO_RS03635: mannose ABC transporter, substrate-binding component

• UniProt sequence D8IZC6: SubName: Full=ABC-type sugar transport system, periplasmic component protein {ECO:0000313|EMBL:ADJ62246.1};
• Comment: The Herbaspirillum seropedicae system (3 components)
• Total: 1 characterized proteins

HSERO_RS03640: mannose ABC transporter, ATPase component

• UniProt sequence D8IZC7: RecName: Full=Ribose import ATP-binding protein RbsA {ECO:0000256|HAMAP-Rule:MF_01716}; EC=7.5.2.7 {ECO:0000256|HAMAP-Rule:MF_01716};
• Total: 1 characterized proteins

HSERO_RS03645: mannose ABC transporter, permease component

• UniProt sequence D8IZC8: SubName: Full=ABC-type sugar transport system, permease component protein {ECO:0000313|EMBL:ADJ62248.1};
• Total: 1 characterized proteins

STP6: mannose:H+ symporter

• Curated sequence CH_091493: sugar transport protein 6. Sugar transport protein 6; Hexose transporter 6. High affinity monosaccharide (KM ≈ 20 µM):H+ symporter, Stp6 (takes up glucose, 3-O-methylglucose, mannose, fructose, galactose and to a lesser extent, xylose and ribulose.
• Curated sequence Q9LT15: The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4
• Total: 2 characterized proteins

gluP: mannose:Na+ symporter

• Curated sequence O25788: The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity)
• Curated sequence 6936374: D-mannitol and D-mannose transporter (MFS superfamily)
• Total: 2 characterized proteins

glcP: mannose:H+ symporter

• Curated sequence O07563: Glucose/mannose transporter GlcP; Glucose/mannose:H(+) symporter. Glucose/Mannose/Xylose: H+ symporter (Paulsen et al., 1998; G.Gosset, personal communication)
• Total: 1 characterized proteins

MST1: mannose:H+ symporter

• Curated sequence A0ZXK6: The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1
• Total: 1 characterized proteins

manMFS: mannose transporter, MFS superfamily

• Curated sequence AO356_28540: D-mannose and D-mannitol transporter
• Total: 1 characterized proteins

manA: mannose-6-phosphate isomerase

• Curated proteins or TIGRFams with EC 5.3.1.8
• UniProt sequence P29954: RecName: Full=Mannose-6-phosphate isomerase; EC=5.3.1.8; AltName: Full=Phosphohexomutase; AltName: Full=Phosphomannose isomerase; Short=PMI;
• Comment: SMc03111 (P29954) is specifically important for utilizing mannose, which confirms it is mannose 6-phosphate isomerase
• Total: 1 HMMs and 29 characterized proteins

man-isomerase: D-mannose isomerase

• Curated proteins or TIGRFams with EC 5.3.1.7
• Ignore hits to AO353_03400 when looking for 'other' hits (Isomerase for D-mannose and D-mannitol catabolism (probably D-mannose-6-phosphate isomerase or D-mannose isomerase))
• Ignore hits to Pf1N1B4_597 when looking for 'other' hits (Isomerase for D-mannose and D-mannitol catabolism (probably D-mannose-6-phosphate or D-mannose isomerase))
• Ignore hits to AO356_05200 when looking for 'other' hits (Isomerase for D-mannose and D-mannitol catabolism (probably D-mannose-6-phosphate isomerase or D-mannose isomerase))
• Comment: Ignore some vaguely annotated mannose or mannose-6-phosphate isomerases
• Total: 7 characterized proteins

mannokinase: D-mannose kinase

• Curated proteins or TIGRFams with EC 2.7.1.7
• Curated sequence SMc03109: Mannokinase (EC 2.7.1.7)
• Curated sequence MONOMER-19002: N-acetylglucosamine kinase (EC 2.7.1.59)
• UniProt sequence Q5GAN8: SubName: Full=General specificity hexokinase {ECO:0000313|EMBL:AAT74901.1};
• Comment: SMc03109 was annotated as mannokinase but not given this EC number. rokA (MONOMER-19002) and hexA (Q5GAN8) are hexose kinases, including mannose kinases (PMID:PMC545704)
• Total: 7 characterized proteins

scrK: fructokinase

• Curated proteins or TIGRFams with EC 2.7.1.4
• Ignore hits to Q09123 when looking for 'other' hits (Fructokinase; EC 2.7.1.4)
• Comment: ignore fragmentary sequence of Q09123
• Total: 36 characterized proteins