Classification of Transporters
Pascale Anderle, ISREC
Overview
Classification according to transport mechanism
Examples
TC System
Gene Ontology
PFAM
Summary
Pumps, channels and transporters
Transporters
Secondary transporters
Membrane Transporter Proteins: Classification
Membrane Transport Proteins
Specific Carriers
Selective Channels
Primary Active Transport
ATP-powered pumps
ATPases:
P-type, F-type and ABC-type ATPases
(ABC transporters)
Primary active transport
Energy derived from hydrolysis of ATP to
ADP liberating energy from high energy
phosphate bond
Secondary Active Transport
Facilitated Diffusion
Uniporters
Glut1-5
Facilitated diffusion
Like any diffusion, transport from an area of
higher concentration to lower concentration.
Passive transport is powered by the potential
energy of a concentration gradient and does
not require the expenditure of metabolic
energy
Symporters
Antiporters
Pept1
NHE
Secondary active transport
Use of energy from another source-another secondary diffusion
gradient set up across the membrane using another ion.
Because this secondary diffusion gradient initially established
using an ion pump, as in primary active transport, the energy is
ultimately derived from the same source-ATP hydrolysis.
Channels
Transport water or specific types of ions down their concentration or electric
potential gradients
Energetically favorable reaction
Form protein-lined passageway across the membrane through which multiple
water molecules or ions move simultaneously at a very rapid rate—up to 108 per
second
Plasma membrane of all animal cells contains potassium-specific channel
proteins that are generally open and are critical to generating the normal,
resting electric potential across the plasma membrane
Many other types of channel proteins are usually closed, and open only in
response to specific signals
Uniporters
Transport is specific and saturable
Facilitated “low resistance” diffusion:
– Down the concentration gradient
– Accelerates reaction that is already thermodynamically favored
Reversible
Rate much higher than passive diffusion:
- Molecule never in contact with hydrophobic core of the membrane
Uniporters: Example GLUT1
Facilitated vs. passive diffusion
Mechanism of transport
Secondary transporters
Couple the movement of one type of ion or molecule against its concentration
gradient to the movement of a different ion or molecule down its concentration
gradient
Ability to transport two different solutes simultaneously 
also called co-transporters
Mediate coupled reactions in which an energetically unfavorable reaction coupled
to energetically favorable reaction
Catalyze “uphill” movement of certain molecules 
often referred to as “active transporters”, but unlike pumps, do
not hydrolyze ATP (or any other molecule) during transport
Symporters: Example Pept1
Antiporters: Example NHE
Pumps
Use the energy of ATP hydrolysis to move ions or small molecules across a membrane against a
chemical concentration gradient or electric potential.
Overall reaction—ATP hydrolysis and the “uphill” movement of ions or small molecules—is energetically
favorable
P, F, and V classes transport ions only, whereas the ABC superfamily class transports small molecules as
well as ions.
Pumps: Example MDR1
TC System: Function/Phylogenetic
Milton Saier et al. (http://tcdb.ucsd.edu/tcdb/)
Functional/phylogenetic system
 Analogous to the Enzyme Commission (EC) system for classification of
enzymes, except that it incorporates both functional and phylogenetic
information. EC strictly functional.
Designed for classification of all transmembrane transport protein found in living
organism on Earth
Nearly 400 families
Affiliation with a family requires rigorous statistical criteria of homology (Saier
1994).
 Comparison over 60 residues
TC System II: Function/Phylogenetic
1. Channels/Pores
1.A. α-Type channels
1.B. β-Barrel porins
1.C. Pore-forming toxins
(proteins and peptides
1.D. Non-ribosomally
synthesized channel
2. Electrochemical Potentialdriven Transporters
2.A. Porters
Uniporters, symporters, antiporters
2.B. Nonribosomally synthesized
porters
3. Primary Active Transporters
4. Group Translocators
5. Transport Electron Carriers
8. Accessory Factors Involved in Transport
9. Incompletely Characterized Transport Systems
2.C. Ion-gradient-driven
energizers
1.E. Holins
Gene Ontology Consortium
GO Output
Cellular Component
L3
L3
L4 GO:X
Molecular Function
L3
L3 GO:Y
Biological processes
L3 GO:Z
L3
L4 GO:Y
ABCB1
Two pragmatic purposes of ontology:
1. Facilitate communication between people and
organizations
2. Improve interoperability between systems
Ontologies are structured vocabularies in the form of
directed acyclic graphs (DAGs) that represent a network
in which each term may be a “child” of one or more than one
”parent”.
Annotation in GO: Porters
ABC Superfamily in GO
07.06.2004
27.09.2004
Classification in Biological Processes
Human Genome Organization: HUGO
The Human Genome Organization (HUGO) Nomenclature Committee Database has as a goal to make sure that
each symbol is unique, and ensures that each gene locus is only given one approved gene symbol
In HUGO Nomenclature Committee Database:
SLC series: Currently 43 families and 298 transporter genes
Non-SLC human transport-related genes:
ATP-driven transporters
Channels
Ionotropic receptors
Aquaporins
Transporter and channel subunits
auxiliary/regulatory transport proteins
PFAM Database
Database of protein domain families
Contains curated multiple sequence alignments for each family, as well as profile hidden
Markov models (profile HMMs) for finding these domains in new sequences
Contains functional annotation, literature references and database links for each family
There are two multiple alignments for each Pfam family:
1. Seed alignment that contains a relatively small number of representative
members of the family
2. The full alignment that contains all members in the database that can be
detected
The profile HMM is built from the seed alignment using the HMMER package (see
http://hmmer.wustl.edu/ ), which is then used to search the pfamseq sequence database
Position specific iterative BLAST (PSI-Blast): Position specific scoring matrix (PSSM) is
constructed (automatically) from a multiple alignment of the highest scoring hits in an
initial BLAST search. The PSSM is generated by calculating position-specific scores for
each position in the alignment. Highly conserved positions receive high scores and
weakly conserved positions receive scores near zero. The profile is used to perform a
second (etc.) BLAST search and the results of each "iteration" used to refine the profile.
This iterative searching strategy results in increased sensitivity.
Summary: Example Pept1
Mechanism
HUGO
TC
Secondary active transporter
SLC series
2. Electrochemical Potentialdriven transporters
Symporter
SLC15 Family
Proton oligopeptide cotransporter
SLC15A1
GO
Molecular function
X transporter activity
XX carrier activity
XXX electrochemical potential-driven
XXXX porter
XXXXX proton-dependent oligopeptide
XXXXXX peptide\:hydrogen symporter
Biological process
X cellular process
XX cellular physiologcial process
XXX cell growth and/or maintenance
XXXX transport
XXXXX peptide transport
XXXXXX oligopeptide transport
XXXXX symporter
XXXXXX solute\:hydrogen symporter
XXXXXXX peptide\:hydrogen symporter
X physiological process
XX cellular physiological process
XXX cell growth and/or maintenance
XXXX transport
XXXXX peptide transport
XXXXXX oligopeptide transport
XX peptide transporter
XXX oligopeptide transporter
XXXX proton-dependent oligopeptide
XXXXX peptide\:hydrogen symporter
XXX organismal physioligcal process
XXXX digestion
2.A. Porters
Uniporters, symporters,
antiporters
2.A.17 The Proton-dependent
Oligopeptide Transporter (POT)
Family
2.A.17.4.1
Peptide:H+ symporter
PFAM
Major Facilitator Superfamily Clan
PTR2 Domain
POT Family
Peptide transporter 1
Short description of TC families I
4 Group Translocators
PEP-dependent, phosphoryl transfer-driven group translocators. Transport systems of the bacterial phosphoenolpyruvate:sugar
phosphotransferase system are the only recognized group translocators included in TC category 4. The product of the reaction, derived
from extracellular sugar, is a cytoplasmic sugar-phosphate. The enzymatic constituents, catalyzing sugar phosphorylation, are superimposed
on the transport process in a tightly coupled process.
5 Transport Electron Carriers
Transmembrane electron flow systems. Systems that catalyze electron flow across a biological membrane, from donors localized to one side
of the membrane to acceptors localized on the other side, are grouped into TC category 5. These systems contribute to or subtract from the
membrane potential, depending on the direction of electron flow. They are therefore important to cellular energetics.
8 Accessory Factors Involved in Transport
Auxiliary transport proteins. Proteins that function with or are complexed to known transport proteins are included in this category. An
example would be the membrane fusion proteins that facilitate transport across the two membranes of the Gram-negative bacterial cell
envelope in a single step driven by the energy source (ATP or the pmf) utilized by a cytoplasmic membrane transporter. Energy coupling
and regulatory proteins that do not actually participate in transport represent other possible examples. In some cases auxiliary proteins are
considered to be part of the transport system with which they function, and in such cases no distinct entry in category 8 is provided.
9 Incompletely Characterized Transport Systems
Transporters of unknown classification. Transport protein families of unknown classification are grouped under TC category 9. Permeases
within families maintained in the 9A class are of unknown mode of transport or energy-coupling mechanism, but at least one member of
each of these families has clearly been shown to function as a transporter. These families will be classified elsewhere when the transport
process and energy-coupling mechanism are characterized. Putative transport protein families are grouped under TC number 9B if they are
putative transporters in which no family member is an established transporter. The family will either be classified elsewhere when the
transport function of a member becomes established or will be eliminated from the TC classification system if the proposed transport
function is disproven. These families include a member or members for which a transport function has been suggested, but evidence for
such a function is not yet compelling. Functionally characterized transporters for which sequences and/or family association are not
available are grouped in class 9C.
Short description of TC families II
1.D Non-ribosomally synthesized channels
Non-ribosomally synthesized channels. These molecules, often chains of L- and D-amino acids as well as other small molecular building
blocks such as hydroxy acids (i.e., lactate), form oligomeric transmembrane ion channels. Voltage may induce channel formation by
promoting assembly of the oligomeric transmembrane pore-forming structure. These depsipeptides are often made by bacteria and fungi as
agents of biological warfare. Other substances, completely lacking amino acids, are also capable of channel-formation.
1.E Holins
Holins consist of about forty distinct families of proteins that exhibit common structural and functional characteristics but which do not exhibit
statistically significant sequence similarity between members of distinct families. They are encoded within the genomes of Gram-positive and Gramnegative bacteria as well as those of the bacteriophage of these organisms. Their primary function appears to be transport of murein hydrolases across the
cytoplasmic membrane to the cell wall where these enzymes hydrolyze the cell wall polymer as a prelude to cell lysis. When chromosomally encoded,
these enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell
death. Some may catalyze export of nucleases.
2.B Nonribosomally synthesized porters
Non-ribosomally synthesized porters. These substances, like non-ribosomally synthesized channels, may be depsipeptides or non-peptidelike substances. They complex a cation in their hydrophilic interior and facilitate translocation of the complex across the membrane,
exposing their hydrophobic exterior, by moving from one side of the bilayer to the other. If the free porter can cross the membrane in the
uncomplexed form, the transport process can be electrophoretic, but if only the complex crosses the membrane, transport is electroneutral.
2.C Ion-gradient-driven energizers
Ion gradient-driven energizers. Normally, outer membrane porins (1.B) of Gram-negative bacteria catalyze passive transport of solutes
across the membrane, but coupled to eeenergizers,, they may accumulate their substrates in the periplasm against large concentration
gradients. These energizers use the ppproton motive force (pmf) across the cytoplasmic membrane, probably by allowing the
electrophoretic transport of protons, and conveying conformational change to the outer membrane receptor/porins. Homologous energizers
drive bacterial flagellar motility. The mechanism is poorly understood, but these energizers undoubtedly couple proton (H+) or sodium
(Na+) fluxes through themselves to the energized process.