Definition of D-xylose catabolism

As rules and steps, or see full text

Rules

Overview: Xylose degradation in GapMind is based on MetaCyc pathways I via D-xylulose (link), II via xylitol (link), III or V via 2-dehydro-3-deoxy-D-arabinonate (DKDP) dehydratase (link, link), IV via DKDP aldolase (link), as well as another pathway via DKDP dehydrogenase (PMC6336799).

• all:
  • xylose-transport, xylA and xylB
  • or xylose-transport, xyrA, xdhA and xylB
  • or xylose-transport, xdh, xylC, xad, kdaD and dopDH
  • or xylose-transport, xdh, xylC, xad, DKDP-aldolase, glycolaldehyde-dehydrogenase, gyaR and glcB
  • or xylose-transport, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR and glcB
  • Comment: In pathway I, isomerase xylA forms D-xylulose and kinase xylB forms D-xylulose 5-phosphate, an intermediate in the pentose phosphate pathway. In pathway II, the reductase xyrA forms xylitol, the dehydrogenase xdhA forms xylitol, and the kinase xylB forms D-xylulose 5-phosphate. (This pathway is only reported in fungi.) In pathway III or V, dehydrogenase xdh forms xylonolactone, lactonase xylC forms D-xylonate, dehydratase xad forms 2-dehydro-3-deoxy-D-arabinonate, dehydratase kdaD forms 2,5-dioxopentanoate (also known as α-ketoglutarate semialdehyde), and dopDH forms 2-oxoglutarate, an intermediate in the TCA cycle. (Pathway III has a 1,4-lactone intermediate, while pathway V has a 1,5-lactone intermediate; GapMind does not distinguish these.) In pathway IV, xdh and xylC form D-xylonate, dehydratase xad forms 2-dehydro-3-deoxy-D-arabinonate (DKDP), and an aldolase forms pyruvate and glycolaldehyde; glycolaldehyde is oxidized to glycolate and to glyoxylate, and assimilated by malate synthase (glcB). Alternatively, after DKDP is formed, a dehydrogenase forms 5-hydroxy,2-4-dioxopentanonate (HDOP), and a hydrolase forms pyruvate and glycolate (PMC6336799); the glycolate is oxidized to glyoxylate and converted to malate.
• glycolaldehyde-dehydrogenase:
  • aldA
  • or aldox-large, aldox-med and aldox-small
• xylose-transport:
  • xylT
  • or gal2
  • or glcP
  • or Echvi_1871
  • or xylF, xylG and xylH
  • or xylF_Tm, xylE_Tm and xylK_Tm
  • or araV, araU, araT and araS
  • or gtsA, gtsB, gtsC and gtsD
  • Comment: Transporters were identified using query: transporter:D-xylose:xylose:CPD-15377

Steps

xylT: D-xylose transporter

• Curated sequence O52733: D-xylose transporter; D-xylose-proton symporter. The D-xylose:H+ symporter, XylT (Km=220 μM; inhibited competitively by 6-deoxyglucose (Ki=220 μM), but not by other sugars tested)
• Curated sequence CH_091400: low-affinity glucose transporter HXT4. Low-affinity glucose transporter HXT4; Low-affinity glucose transporter LGT1. Low affinity, constitutive, glucose (hexose; xylose) uniporter, Hxt4 (LGT1; Rag1) (also transports arsenic trioxide [As(OH)3] as do Hxtl, 3, 5, 7 and 9)
• 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 CH_109760: D-xylose-proton symporter. D-xylose-proton symporter; D-xylose transporter. Xylose (xylopyranose):H+ symporter of 491 aas and 12 TMSs. D-xylose:H⁺ symporter. D-xylose:H⁺ symporter
• Curated sequence P0AE24: Arabinose-proton symporter; Arabinose transporter. Arabinose (xylose; galactose):H+ symporter, AraE (low affinity high capacity). arabinose:H⁺ symporter. arabinose:H⁺ symporter
• Curated sequence P96710: Arabinose-proton symporter; Arabinose transporter. L-arabinose:proton symporter, AraE (Sa-Nogueira and Ramos, 1997). Also transports xylose, galactose and α-1,5 arabinobiose
• Curated sequence C4B4V9: Arabinose/xylose transporter, AraE
• Curated sequence Q0WWW9: D-xylose-proton symporter-like 3, chloroplastic
• Curated sequence Q2MDH1: Glucose/xylose facilitator-1, GXF1 (functions by sugar uniport; low affinity
• Curated sequence Q2MEV7: Glucose/xylose: H+ symporter, Gsx1
• Curated sequence Q64L87: The xylose facilitator, Xylhp
• Curated sequence Q9XIH7: The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida
• UniProt sequence A0A0H3C6H3: SubName: Full=Glucose/fructose transport protein {ECO:0000313|EMBL:ACL94322.2};
• Comment: Fitness data identified CCNA_00857 (CC0814; A0A0H3C6H3) as the xylose transporter in Caulobacter crescentus, consistent with a previous report (PMC2168598).
• Total: 13 characterized proteins

gal2: galactose/glucose/xylose uniporter

• Curated sequence CH_091029: galactose transporter. Galactose, glucose uniporter, Gal2. Also transports xylose
• Total: 1 characterized proteins

glcP: glucose/mannose/xylose: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

Echvi_1871: sodium/xylose cotransporter

• UniProt sequence L0FZF3: SubName: Full=SSS sodium solute transporter {ECO:0000313|EMBL:AGA78126.1};
• Comment: Echvi_1871 (L0FZF3) seems to be a xylose transporter as well as a glucose/galactose transporter.
• Total: 1 characterized proteins

xylF: ABC transporter for xylose, substrate binding component xylF

• Curated sequence CH_003787: D-xylose ABC transporter, periplasmic D-xylose-binding protein. XylF aka XYLT aka B3566, component of Xylose porter. xylose ABC transporter periplasmic binding protein (EC 7.5.2.13; EC 7.5.2.10). xylose ABC transporter periplasmic binding protein (EC 7.5.2.13)
• Curated sequence A6LW10: D-xylose ABC transporter, periplasmic substrate-binding protein, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas
• Curated sequence P25548: CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
• Curated sequence G4FGN5: LacI family transcriptional regulator, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
• Ignore hits to P54083 when looking for 'other' hits (Multiple sugar-binding periplasmic protein SbpA; Sugar-binding protein A)
• Comment: T. maritima has a diverged SBP, Tmari_1858 (G4FGN5). Tmari_1858 is sometimes annotated as gluE, and is glucose induced. But the Km for xylose is quite low, so, considered it a xylose transporter as well. Ignore P54083 (sbpA from A. brasilensis), not known if it transports xylose or not; close homolog HSERO_RS05190 is mildly important for fitness during growth on xylose, so, it may transport xylose.
• Total: 4 characterized proteins

xylG: ABC transporter for xylose, ATP-binding component xylG

• Curated sequence P37388: Xylose import ATP-binding protein XylG; EC 7.5.2.10. D-xylose ABC transporter, ATP-binding protein; EC 3.6.3.17. XylG aka B3567, component of Xylose porter. xylose ABC transporter ATP binding subunit (EC 7.5.2.13; EC 7.5.2.10). xylose ABC transporter ATP binding subunit (EC 7.5.2.13)
• Curated sequence A6LW11: Xylose import ATP-binding protein XylG, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas
• Curated sequence G4FGN3: Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
• Curated sequence O05176: GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
• Total: 4 characterized proteins

xylH: ABC transporter for xylose, permease component xylH

• Curated sequence A6LW12: Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas
• Curated sequence CH_024441: D-xylose ABC transporter, permease protein. Xylose transport system permease protein XylH aka B3568, component of Xylose porter. xylose ABC transporter membrane subunit (EC 7.5.2.13; EC 7.5.2.10). xylose ABC transporter membrane subunit (EC 7.5.2.13)
• Curated sequence G4FGN4: Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
• Curated sequence O05177: GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
• Total: 4 characterized proteins

xylF_Tm: ABC transporter for xylose, permease component xylF

• Curated sequence Q9WXW7: ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR
• Comment: TC 3.A.1.2.18 describes another ABC transporter for xylose in T. maritima: Q9WXW7 = TM0112 = XylF, the permease subunit; Q9WXW9 = TM0114 = XylE, the SBP, reported high affinity for xylose (PMC1392961); Q9WXX0 = TM0115 = xylK is the ATPase-binding component. Also TM0113 is a putative xylanase. (Only the SBP seems to be characterized but the clustering of these genes with each other and other xylose-related genes is quite suggestive.) TC 3.A.1.2.18 also includes Q9WXW0 = TM0105, for which TCDB cites Nanavati et al (PMC1392961), but that paper does not mention this gene. Probably a curation error.
• Total: 1 characterized proteins

xylE_Tm: ABC transporter for xylose, substrate binding component xylE

• UniProt sequence Q9WXW9: SubName: Full=Sugar ABC transporter, periplasmic sugar-binding protein {ECO:0000313|EMBL:AAD35208.1};
• Total: 1 characterized proteins

xylK_Tm: ABC transporter for xylose, ATP binding component xylK

• UniProt sequence Q9WXX0: RecName: Full=Ribose import ATP-binding protein RbsA 1 {ECO:0000255|HAMAP-Rule:MF_01716}; EC=7.5.2.7 {ECO:0000255|HAMAP-Rule:MF_01716};
• Total: 1 characterized proteins

araV: component of Arabinose, fructose, xylose porter

• Curated sequence Q97UF2: AraV, component of Arabinose, fructose, xylose porter
• Comment: AraVUTS (TC 3.A.1.1.14) from Sulfolobus solfataricus
• Total: 1 characterized proteins

araU: component of Arabinose, fructose, xylose porter

• Curated sequence Q97UF3: AraU, component of Arabinose, fructose, xylose porter
• Total: 1 characterized proteins

araT: component of Arabinose, fructose, xylose porter

• Curated sequence Q97UF4: AraT, component of Arabinose, fructose, xylose porter
• Total: 1 characterized proteins

araS: component of Arabinose, fructose, xylose porter

• Curated sequence Q97UF5: AraS, component of Arabinose, fructose, xylose porter
• Total: 1 characterized proteins

gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA

• Curated sequence GFF4324: ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component
• Ignore hits to Q88P38 when looking for 'other' hits (GtsA (GLcE), component of Glucose porter, GtsABCD)
• Comment: GtsABCD from P. fluorescens WCS417 (PS417_22130:PS417_22145) is very important for utilization of both glycose and xylose. Similar systems in other Pseudomonas have been reported as glucose transporters. In P. putida, after enzymes for xylose catabolism were introduced and the strain was evolved for growth on xylose, GtsABCD were required for xylose utilization, although there were two point mutations in GtsA, so it is not certain if the wild-type P. putida GtsA binds xylose efficiently (see PMC3340264). The P. putida system is marked ignore. GtsA = PS417_22145 = GFF4324
• Total: 1 characterized proteins

gtsB: xylose ABC transporter, permease component 1 GtsB

• Curated sequence GFF4323: ABC transporter for D-Glucose-6-Phosphate, permease component 2
• Ignore hits to Q88P37 when looking for 'other' hits (GtsB (GLcF), component of Glucose porter, GtsABCD)
• Comment: GtsB = PS417_22140 = GFF4323
• Total: 1 characterized proteins

gtsC: xylose ABC transporter, permease component 2 GtsC

• Curated sequence GFF4322: ABC transporter for D-Glucose-6-Phosphate, permease component 1
• Ignore hits to Q88P36 when looking for 'other' hits (GtsC (GLcG), component of Glucose porter, GtsABCD)
• Comment: GtsC = PS417_22135 = GFF4322
• Total: 1 characterized proteins

gtsD: xylose ABC transporter, ATPase component GtsD

• Curated sequence GFF4321: ABC transporter for D-Glucose-6-Phosphate, ATPase component
• Ignore hits to Q88P35 when looking for 'other' hits (GtsD (GLcK), component of Glucose porter, GtsABCD)
• Comment: GtsD = PS417_22130 = GFF4321
• Total: 1 characterized proteins

xylA: xylose isomerase

• Curated proteins or TIGRFams with EC 5.3.1.5
• Total: 2 HMMs and 20 characterized proteins

xylB: xylulokinase

• Curated proteins or TIGRFams with EC 2.7.1.17
• UniProt sequence L0FZT0: SubName: Full=Pentulose/hexulose kinase {ECO:0000313|EMBL:AGA78130.1};
• UniProt sequence Q97FW4: RecName: Full=Xylulose kinase {ECO:0000256|HAMAP-Rule:MF_02220, ECO:0000256|RuleBase:RU364073}; Short=Xylulokinase {ECO:0000256|HAMAP-Rule:MF_02220, ECO:0000256|RuleBase:RU364073}; EC=2.7.1.17 {ECO:0000256|HAMAP-Rule:MF_02220, ECO:0000256|RuleBase:RU364073};
• UniProt sequence Q8A9M3: SubName: Full=Xylulose kinase (Xylulokinase) {ECO:0000313|EMBL:AAO75899.1};
• Comment: Echvi_1875 (L0FZT0) is annotated as xylulose kinase and has its strongest phentoypes on xylose. CA_C2612 (Q97FW4) from Clostridium acetobutylicum was proven to be xylulose kinase (PMC2873477). BT0792 (Q8A9M3) has its strongest phenotypes on xylose.
• Total: 1 HMMs and 21 characterized proteins

xyrA: xylitol reductase

• Curated proteins or TIGRFams with EC 1.1.1.307
• Total: 15 characterized proteins

xdhA: xylitol dehydrogenase

• Curated proteins or TIGRFams with EC 1.1.1.9
• Ignore hits to items matching 1.1.1.14 when looking for 'other' hits
• Ignore hits to items matching xylulose reductase when looking for 'other' hits
• Comment: L-iditol 2-dehydrogenases (EC 1.1.1.14) often act on xylitol as well, so are ignored. There's also some xylulose reductases annotated but without an EC number.
• Total: 24 characterized proteins

xdh: D-xylose dehydrogenase

• Curated proteins or TIGRFams with EC 1.1.1.179
• Curated proteins or TIGRFams with EC 1.1.1.175
• UniProt sequence A0A4R8NY47: SubName: Full=NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) {ECO:0000313|EMBL:TDY98647.1};
• Comment: Watanabe et al 2019 (PMC6336799) show that C785_RS00860 = WP_034330287.1 = A0A4R8NY47 is D-xylose dehydrogenase (xdh). Another issue is that xdh from Haloferax volcanii (HVO_B0028; D4GP29) is reported to form xylono-1,4-lactone, (Sutter et al 2017, PMID:28854683), but this is not reflected in the databases, and for some (many?) xylose dehydrogenases, it is uncertain which lactone they form. So, both forms of D-xylose dehydrogenase are included in "xdh."
• Total: 15 characterized proteins

xylC: xylonolactonase

• Curated proteins or TIGRFams with EC 3.1.1.110
• Curated proteins or TIGRFams with EC 3.1.1.68
• Ignore hits to items matching 3.1.1.15 when looking for 'other' hits
• Comment: EC 3.1.1.110 is the 1,5-lactonase; EC 3.1.1.68 is the 1,4-lactonase; both are included in "xylC." xylono-1,4-lactonase is sometimes given EC 3.1.1.15 (L-arabinino-1,4-lactonase) so ignore those; indeed HVO_B0030 = metacyc::MONOMER-20630 has both 1,4-lactonase activities (PMID:28854683).
• Total: 3 characterized proteins

xad: D-xylonate dehydratase

• Curated proteins or TIGRFams with EC 4.2.1.82
• UniProt sequence D8IWS7_HERSS: SubName: Full=Dihydroxyacid dehydratase/phosphogluconate dehydratase protein {ECO:0000313|EMBL:ADJ65964.1}; EC=4.2.1.9 {ECO:0000313|EMBL:ADJ65964.1};
• Comment: Watanabe et al (PMC6336799) show that C785_RS00855 = WP_039783171.1 = UPI0004007277 is D-xylonate dehydratase (xad); this is 98% identical to D8IWS7_HERSS, so use that identifier.
• Total: 9 characterized proteins

kdaD: 2-keto-3-deoxy-D-arabinonate dehydratase

• Curated proteins or TIGRFams with EC 4.2.1.141
• Comment: Watanabe et al (PMC6336799) show that C785_RS13680 = WP_039786859.1 = UPI00041852D2 is DKDP dehydratase (kdaD). Is 98% identical to HSERO_RS19360, which is included via reannotations.
• Total: 6 characterized proteins

dopDH: 2,5-dioxopentanonate dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.26
• Total: 19 characterized proteins

DKDP-aldolase: 2-dehydro-3-deoxy-D-arabinonate aldolase

• Curated proteins or TIGRFams with EC 4.1.2.28
• Ignore hits to items matching 4.1.2.55 when looking for 'other' hits
• Comment: A number of EC 4.1.2.55 enzymes are similar but are promiscuous and are likely to have this activity as well. This includes Q97U28 which is nearly identical to the promiscuous KDGA_SACSO (O54288), but is not annotated with this activity.
• Total: 3 characterized proteins

aldox-large: (glycol)aldehyde oxidoreductase, large subunit

• Curated sequence MONOMER-18071: glycolaldehyde oxidoreductase large subunit
• Curated sequence Q4J6M3: Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8
• Ignore hits to items matching 1.2.99.8 when looking for 'other' hits
• Comment: glycolaldehyde oxidoreductase has multiple subunits and no EC number (Q97VI4, Q97VI7, Q97VI6). This is an inference from close homologs from S. acidocaldarius, which have demonstrated activity on glyceraldehyde-3-phosphate, glyceraldehyde, and acetaldehyde, but not on glycolaldehyde itself, so there's no proof that these genes provide the activity. Related enzymes in EC 1.2.99.8 are promiscuous, may well have this activity, so ignore.
• Total: 2 characterized proteins

aldox-med: (glycol)aldehyde oxidoreductase, medium subunit

• Curated sequence MONOMER-18072: glycolaldehyde oxidoreductase medium subunit
• Curated sequence Q4J6M6: Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8
• Ignore hits to items matching 1.2.99.8 when looking for 'other' hits
• Total: 2 characterized proteins

aldox-small: (glycol)aldehyde oxidoreductase, small subunit

• Curated sequence MONOMER-18073: glycolaldehyde oxidoreductase small subunit
• Curated sequence Q4J6M5: Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8
• Ignore hits to items matching 1.2.99.8 when looking for 'other' hits
• Total: 2 characterized proteins

aldA: (glycol)aldehyde dehydrogenase

• Curated proteins or TIGRFams with EC 1.2.1.21
• Comment: There's also glycolaldehyde dehydrogenase, EC 1.2.1.21 (aldA), with a single subunit
• Total: 1 characterized proteins

gyaR: glyoxylate reductase

• Curated proteins or TIGRFams with EC 1.1.1.26
• Ignore hits to items matching 1.1.1.79 when looking for 'other' hits
• Comment: The NADP based glyoxylate reductase (EC 1.1.1.79) is probably biased in the wrong direction for glycolate oxidation, so do not include, but ignore homology to it.
• Total: 6 characterized proteins

glcB: malate synthase

• Curated proteins or TIGRFams with EC 2.3.3.9
• Ignore hits to items matching 4.1.3.24 when looking for 'other' hits
• Comment: Besides the standard enzyme, there's an archaeal enzyme that is sometimes annotated as EC 4.1.3.24, but that only includes the formation of malyl-CoA, not the cleavage to malate.
• Total: 2 HMMs and 22 characterized proteins

DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase

• UniProt sequence A0A4P7ABK7: SubName: Full=SDR family oxidoreductase {ECO:0000313|EMBL:QBP77113.1};
• Comment: C785_RS13675 = WP_039786858.1 = A0A4P7ABK7 is the DKDP 4-dehydrogenase (PMC6336799).
• Total: 1 characterized proteins

HDOP-hydrol: 5-hydroxy-2,4-dioxopentanonate hydrolase

• UniProt sequence A0A2E7P912: SubName: Full=FAA hydrolase family protein {ECO:0000313|EMBL:MBO18215.1};
• Ignore hits to BPHYT_RS34210 when looking for 'other' hits (2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-))
• Ignore hits to SM_b21112 when looking for 'other' hits (L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase)
• Comment: C785_RS20550 = WP_039788920.1 = A0A2E7P912 is the HDOP hydrolase (PMC6336799). This enzyme is also similar to SM_b21112, thought to be L-2,4-diketo-3-deoxyrhamnonate hydrolase and 2,4-dioxopentanoate hydrolase; it is plausible that SM_b21112 acts on HDOP as well. Similarly for BPHYT_RS34210 (thought to act on 2,4-diketo-3-deoxy-L-fuconate = L-2,4-diketo-3-deoxyrhamnonate). Both of these homologs are ignored.
• Total: 1 characterized proteins