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Title :   CRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) MUTATION W48F, F200T

Authors :   P. Nollert, L. J. W. Miercke, J. O'Connell, R. M. Stroud

Date :   08 Apr 02 (Deposition) - 08 May 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Glycerol-Conducting Membrane Channel Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Tajkhorshid, P. Nollert, M. O. Jensen, L. J. Miercke, J. O'Connell, R. M. Stroud, K. Schulten
Control Of The Selectivity Of The Aquaporin Water Channel Family By Global Orientational Tuning.
Science V. 296 525 2002
PubMed-ID: 11964478 | Reference-DOI: 10.1126/SCIENCE.1067778
(for further references see the PDB file header)

Molecule 1 - GLYCEROL UPTAKE FACILITATOR PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI K12
	Expression System Strain	:	K12
	Expression System Taxid	:	83333
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	AQUAGLYCEROPORIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	BOG	8	Ligand/Ion	B-OCTYLGLUCOSIDE
2	GOL	8	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:102 , TYR A:105 , TYR A:109 , PHE A:113 , LEU A:216 , ALA A:217 , GLY A:218 , HOH A:505	BINDING SITE FOR RESIDUE BOG A 473
2	AC2	SOFTWARE	VAL A:126 , GLU A:127 , PHE A:208 , ASN A:221 , PHE A:233 , HOH A:479 , HOH A:523	BINDING SITE FOR RESIDUE BOG A 474
3	AC3	SOFTWARE	GLU A:43 , HOH A:522 , HOH A:531	BINDING SITE FOR RESIDUE MG A 301
4	AC4	SOFTWARE	TRP A:42 , HOH A:521 , HOH A:522	BINDING SITE FOR RESIDUE MG A 302
5	AC5	SOFTWARE	VAL A:52 , HIS A:66 , ASN A:68 , ILE A:187 , ASN A:203 , HOH A:517	BINDING SITE FOR RESIDUE GOL A 475
6	AC6	SOFTWARE	TYR A:138 , GLY A:195 , PRO A:196 , GLY A:199 , HOH A:510 , HOH A:529	BINDING SITE FOR RESIDUE GOL A 476

(no "SS Bond" information available for 1LDF)

(no "Cis Peptide Bond" information available for 1LDF)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GLPF_ECOLI_001 *	V	126	I	GLPF_ECOLI	---	---	A	V	126	I
2	UniProt	VAR_GLPF_ECOLI_002 *	M	160	I	GLPF_ECOLI	---	---	A	M	160	I
3	UniProt	VAR_GLPF_ECOLI_003 *	G	239	S	GLPF_ECOLI	---	---	A	G	239	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GLPF_ECOLI_001 *	V	126	I	GLPF_ECOLI	---	---	A	V	126	I
2	UniProt	VAR_GLPF_ECOLI_002 *	M	160	I	GLPF_ECOLI	---	---	A	M	160	I
3	UniProt	VAR_GLPF_ECOLI_003 *	G	239	S	GLPF_ECOLI	---	---	A	G	239	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIP	PS00221	MIP family signature.	GLPF_ECO57	66-74	1	A:66-74
				GLPF_ECOL6	66-74	1	A:66-74
				GLPF_ECOLI	66-74	1	A:66-74

Biological Unit 1 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIP	PS00221	MIP family signature.	GLPF_ECO57	66-74	4	A:66-74
				GLPF_ECOL6	66-74	4	A:66-74
				GLPF_ECOLI	66-74	4	A:66-74

(no "Exon" information available for 1LDF)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:254
 aligned with GLPF_ECO57 | P0AER2 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:254
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
           GLPF_ECO57     6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHL 259
               SCOP domains d1ldfa_ A: Glycerol uptake facilitator protein GlpF                                                                                                                                                                                                            SCOP domains
               CATH domains 1ldfA00 A:6-259 Glycerol uptake facilitator protein.                                                                                                                                                                                                           CATH domains
               Pfam domains MIP-1ldfA01 A:6-251                                                                                                                                                                                                                                   -------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------I---------------------------------I------------------------------------------------------------------------------S-------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------MIP      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ldf A   6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIFGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGTAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHL 259
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Chain A from PDB  Type:PROTEIN  Length:254
 aligned with GLPF_ECOL6 | P0AER1 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:254
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
           GLPF_ECOL6     6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHL 259
               SCOP domains d1ldfa_ A: Glycerol uptake facilitator protein GlpF                                                                                                                                                                                                            SCOP domains
               CATH domains 1ldfA00 A:6-259 Glycerol uptake facilitator protein.                                                                                                                                                                                                           CATH domains
               Pfam domains MIP-1ldfA01 A:6-251                                                                                                                                                                                                                                   -------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------I---------------------------------I------------------------------------------------------------------------------S-------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------MIP      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ldf A   6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIFGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGTAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHL 259
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Chain A from PDB  Type:PROTEIN  Length:254
 aligned with GLPF_ECOLI | P0AER0 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:254
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
           GLPF_ECOLI     6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHL 259
               SCOP domains d1ldfa_ A: Glycerol uptake facilitator protein GlpF                                                                                                                                                                                                            SCOP domains
               CATH domains 1ldfA00 A:6-259 Glycerol uptake facilitator protein.                                                                                                                                                                                                           CATH domains
               Pfam domains MIP-1ldfA01 A:6-251                                                                                                                                                                                                                                   -------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------I---------------------------------I------------------------------------------------------------------------------S-------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------MIP      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ldf A   6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIFGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGTAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHL 259
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Aquaporin-like (34)

Superfamily: Aquaporin-like (34)

Family: Aquaporin-like (22)

Protein domain: Glycerol uptake facilitator protein GlpF (4)

Escherichia coli [TaxId: 562] (4)

d1ldfa_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Glycerol uptake facilitator protein (37)

Homologous Superfamily: Glycerol uptake facilitator protein. (37)

Escherichia coli. Organism_taxid: 562. (4)

1ldfA00

A:6-259

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MIP] (17)

Family: MIP (17)

Escherichia coli (strain K12) (11)

MIP-1ldfA01

A:6-251

Asymmetric Unit(hide GO term definitions)

Chain A (GLPF_ECO57 | P0AER2)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (GLPF_ECOL6 | P0AER1)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A (GLPF_ECOLI | P0AER0)

molecular function
	GO:0015254	glycerol channel activity	Enables the facilitated diffusion of glycerol (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0015168	glycerol transmembrane transporter activity	Enables the transfer of glycerol from one side of the membrane to the other. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
	GO:0015250	water channel activity	Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005372	water transmembrane transporter activity	Enables the directed movement of water (H2O) from one side of a membrane to the other.
biological process
	GO:0071288	cellular response to mercury ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
	GO:0009992	cellular water homeostasis	Any process involved in the maintenance of an internal steady state of water within a cell.
	GO:0015793	glycerol transport	The directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0006833	water transport	The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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1lda	CRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITHOUT SUBSTRATE GLYCEROL
1ldi	CRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITHOUT SUBSTRATE GLYCEROL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

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Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (16, 28)

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