Enzymes of Glycolysis

What InterPro tells us: phase II enzymes

Below are examples from InterPro for the enzymes at each step in the second phase of glycolysis, and their family relationships with other proteins.

P00354 Human glyceraldehyde 3-phosphate dehydrogenase entry from InterPro

Interpro Entry	Method accession	Graphical match	Method name
IPR000173	PF00044		Gp_dh_N
IPR000173	PF02800		Gp_dh_C
IPR000173	PR00078		G3PDHDRGNASE
IPR000173	PS00071		GAPDH
IPR006424	TIGR01534		GAPDH-I
Classification	Domain ID	Structural Domains
c.2.1.3	d3gpdg1
d.81.1.1	d3gpdg2

Glyceraldehydes 3-phosphate dehydrogenase (GAPDH) exists as a tetramer of identical subunits, each subunit consisting of two domains: an N-terminal NAD-binding domain and a highly conserved C-terminal catalytic domain.

From the sixth graphical match, you can see that the signatures in InterPro for muscle GAPDH fall into two entries, IPR000173, which represents the GAPDH family, including D-erythrose-4-phosphate dehydrogenase (E4PDH) from proteobacteria, and IPR006424, which is a child of IPR000173 that represents the type I GAPDH family (type II enzymes are limited to Archaea). In all, IPR000173 has three child families in InterPro: type I GAPDH, type II GAPDH and E4PDH.

IPR000173 GAPDH	g	IPR006422 E4PDH
	g	IPR006424 GAPDH type I
	g	IPR006436 GAPDH type II

There are four signatures in IPR000173: PF00044 and PF02800 from the PFAM database, which represent the NAD-binding and the catalytic domains, respectively, PR00078 from the PRINTS database, which uses motifs surrounding the active site of the protein, and PS00071 from the PROSITE database, which uses sequence around a highly conserved cysteine in the middle of the molecule that is involved in forming a covalent phosphoglycerol thioester intermediate. There is one signature in IPR006424, TIGR01534, from the TIGRFAM database, which covers the entire protein sequence.

The remaining two entries in the table are from the structural classification database SCOP (d3gpdg1 and d3gpdg2), both of which are derived from the same PDB entry (3gpd), but which describe the N- and C-terminal domains, respectively.

P00560 Yeast phosphoglycerate kinase entry from InterPro

Interpro Entry	Method accession	Graphical match	Method name
IPR001576	PF00162		PGK
IPR001576	PR00477		PHGLYCKINASE
IPR001576	PS00111		PGLYCERATE_KINASE
IPR001576	SSF53748		PGK
Classification	Domain ID	Structural Domains
3.40.50.1260.1	1qpg01
3.40.50.1270.1	1qpg02
c.86.1.1	d1qpg__

Phosphoglycerate kinase (PGK) exists as a monomer containing two domains: an N-terminal 3-phosphoglycerate-binding domain and a C-terminal nucleotide-binding domain.

From the seventh graphical match, you can see that the signatures in InterPro for PGK fall into a single entry, IPR001576, which represents the PGK family of proteins. There are four signatures in this entry: PF00162 from the PFAM database, SSF53748 from the SUPERFAMILY database, both of which describe the entire protein sequence, PR00477 from the PRINTS database, which uses motifs drawn from short conserved regions in the N- and C-terminal, and hinge regions, and PS00111 from the PROSITE database, which uses a conserved region in the N-terminal domain.

The remaining two entries in the table are from the structural classification databases CATH (1qpg01 and 1qpg02) and SCOP (d1qpg__), where the CATH entry describes each of the two PGK domains separately, while the SCOP entry describes the entire protein.

P00950 Yeast phosphoglycerate mutase entry from InterPro

Interpro Entry	Method accession	Graphical match	Method name
IPR001345	PF00300		PGAM
IPR001345	PS00175		PG_MUTASE
IPR005952	TIGR01258		pgm_1
Classification	Domain ID	Structural Domains
3.40.50.1240.1	1qhfA0
c.60.1.1	d1bq3a_

From the eighth graphical match, you can see that the signatures in InterPro for phosphoglycerate mutase (PGAM) fall into a two entries, IPR001345, which represents the phosphoglycerate and bisphosphoglycerate mutase (PGAM/BPGM) family, two related enzymes that both catalyse phosphotransfer reactions, and IPR005952, which is a child of IPR001345 that represents the phosphoglycerate mutase 1 (PGAM 1) family (those that use 2,3-bisphosphoglycerate as a primer). In all, IPR001345 has three child families in InterPro: fructose-2,6-bisphosphatase (F2,6BPase), phosphohistidine phosphatase sixA (PHP6A), and PGAM 1.

IPR001345 PGM/BPGM	g	IPR003094 F2,6BPase
	g	IPR004449 PHP6A
	g	IPR005952 PGAM 1

There are two signatures in IPR001345: PF00300 from the PFAM database, which was derived from the entire protein sequence, and PS00175 from the PROSITE database, which built the signature around the phosphohistidine residue. IPR005952 has only one signature from the TIGRFAM database, TIGR01258, which describes the entire sequence.

The remaining two entries in the table are from the structural classification databases CATH (1qhfA0) and SCOP (d1bq3a_ ), where both entries describe the entire protein.

P08324 E. coli enolase entry from InterPro

Interpro Entry	Method accession	Graphical match	Method name
IPR000941	PD000902		Enolase
IPR000941	PF00113		Enolase_C
IPR000941	PF03952		Enolase_N
IPR000941	PR00148		ENOLASE
IPR000941	PS00164		ENOLASE
IPR000941	TIGR01060		eno
Classification	Domain ID	Structural Domains
3.20.20.120.1	1e9iA2
3.30.390.10.2	1e9iA1
c.1.11.1	d1e9id1
d.54.1.1	d1e9ia2

From the ninth graphical match, you can see that the signatures in InterPro for enolase fall into a single entry, IPR000941, which represents the enolase family that includes the related proteins mandelate racemase and muconate cylcoisomerase. There are six signatures in this entry: PD000902 from the PRODOM database, TIGR01060 from the TIGRFAM database, both of which cover the entire protein sequence, PF00113 and PF03952 from the PFAM database, which cover the C- and N-terminal domains, respectively, PR00148 from the PRINTS database, which uses motifs drawn from the active site, and PS00164 from the PROSITE database, which uses the best conserved region in the C-terminus.

The remaining four entries in the table are from the structural classification databases CATH (1e9iA2 and 1e9iA1) and SCOP (d1e9id1 and d1e9ia2), where both databases describe the two domains of the protein separately.

P30613 Human pyruvate kinase entry from InterPro

Interpro Entry	Method accession	Graphical match	Method name
IPR001697	PD001009		Pyruvate_kinase
IPR001697	PF00224		PK
IPR001697	PF02887		PK_C
IPR001697	PR01050		PYRUVTKNASE
IPR001697	PS00110		PYRUVATE_KINASE
IPR001697	SSF52935		Pyruvate_kinase
IPR001697	TIGR01064		pyruv_kin
Classification	Domain ID	Structural Domains
b.58.1.1	d1liua1
c.1.12.1	d1liua2
c.49.1.1	d1liua3

All isozymes of pyruvate kinase (PK) appear to be tetramers of identical subunits, where each subunit consists of three domains.

From the tenth graphical match, you can see that the signatures in InterPro for L/R-type PK falls into a single entry, IPR001697, which represents the PK family of proteins. There are seven signatures in this entry: PD001009 from the PRODOM database, TIGR01064 from the TIGRFAM database, both of which describe the entire protein sequence, PF00224 and PF02887 from the PFAM database, which describe the domain architecture of the protein with PF00224 covering the two beta-barrel domains (one inserted within the other) and PF02887 covering the C-terminal a/b domain, SSF52935 from the SUPERFAMILY database, which also covers the C-terminal a/b domain, PR01050 from the PRINTS database, which uses motifs drawn from conserved regions throughout the entire sequence, and PS00110 from the PROSITE database, which uses a conserved region containing a lysine that appears to act as an acid/base catalyst and a glutamic acid involved in binding magnesium.

The remaining three entries in the table are from the structural classification database SCOP (d1liua1, d1liua2 and d1liua3), which describe the three domains of the protein in more detail: d1liua3 describes the C-terminal a/b domain as depicted by PF02887 and SSF52935, while d1liua1 and dliua2 describe the two domains depicted by PF00224, with d1liua2 covering the N-terminal TIM b/a-barrel that is interrupted by an all-b-barrel domain covered by d1liua1.

Next: Table of the enzymes involved in glycolysis

Previous: What InterPro tells us: phase I enzymes