2Y5Y - JenaLib

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Title :   CRYSTAL STRUCTURE OF LACY IN COMPLEX WITH AN AFFINITY INACTIVATOR

Authors :   V. Chaptal, S. Kwon, M. R. Sawaya, L. Guan, H. R. Kaback, J. Abramson

Date :   19 Jan 11 (Deposition) - 15 Jun 11 (Release) - 06 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.38

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)

Keywords :   Transport Protein, Affinity Inactivation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Chaptal, S. Kwon, M. R. Sawaya, L. Guan, H. R. Kaback, J. Abramson
Crystal Structure Of Lactose Permease In Complex With An Affinity Inactivator Yields Unique Insight Into Sugar Recognition.
Proc. Natl. Acad. Sci. Usa V. 108 9361 2011
PubMed-ID: 21593407 | Reference-DOI: 10.1073/PNAS.1105687108
(for further references see the PDB file header)

Molecule 1 - LACTOSE PERMEASE
	Atcc	:	27325
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Vector	:	PET18
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	METHANE-THIO-SULFONIDE-GALACTOSIDE LINKED BY S-S BOND TO C122.
	Strain	:	K-12
	Synonym	:	LACTOSE-PROTON SYMPORT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BA	2	Ligand/Ion	BARIUM ION
2	TGA	2	Ligand/Ion	METHANETHIOSULFONYL-GALACTOSIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	BA	-1	Ligand/Ion	BARIUM ION
2	TGA	2	Ligand/Ion	METHANETHIOSULFONYL-GALACTOSIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:130 , ASN A:204	BINDING SITE FOR RESIDUE BA A 501
2	AC2	SOFTWARE	PHE A:20 , CYS A:122 , TRP A:151 , GLU A:269	BINDING SITE FOR RESIDUE TGA A 701
3	AC3	SOFTWARE	GLU B:130 , ASN B:204	BINDING SITE FOR RESIDUE BA B 501
4	AC4	SOFTWARE	PHE B:20 , CYS B:122 , GLU B:126 , TRP B:151 , GLU B:269	BINDING SITE FOR RESIDUE TGA B 801

(no "SS Bond" information available for 2Y5Y)

(no "Cis Peptide Bond" information available for 2Y5Y)

(no "SAP(SNP)/Variant" information available for 2Y5Y)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MFS	PS50850	Major facilitator superfamily (MFS) profile.	LACY_ECOLI	8-404	2	A:8-403 B:8-404
2	LACY_1	PS00896	LacY family proton/sugar symporters signature 1.	LACY_ECOLI	64-78	2	A:64-78 B:64-78
3	LACY_2	PS00897	LacY family proton/sugar symporters signature 2.	LACY_ECOLI	280-294	2	A:280-294 B:280-294

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MFS	PS50850	Major facilitator superfamily (MFS) profile.	LACY_ECOLI	8-404	2	A:8-403 B:8-404
2	LACY_1	PS00896	LacY family proton/sugar symporters signature 1.	LACY_ECOLI	64-78	2	A:64-78 B:64-78
3	LACY_2	PS00897	LacY family proton/sugar symporters signature 2.	LACY_ECOLI	280-294	2	A:280-294 B:280-294

(no "Exon" information available for 2Y5Y)

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:386
 aligned with LACY_ECOLI | P02920 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:400
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403
           LACY_ECOLI     4 LKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGP 403
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.--------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----MFS  PDB: A:8-403 UniProt: 8-404                                                                                                                                                                                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------------LACY_1         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LACY_2         ------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5y A   4 LKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFSFNAGCPAVEAFIEKVSRRSNFEFGRARMFGAVGWALVASIVGIMFTINNQFVFWLGSGMALILAVLLFFAK--------------ANHSAFSLKLALELFRQPKLWFLSLYVIGVSSTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYITSQFEVRFSATIYLVAFAFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGP 403
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    |    -       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403
                                                                                                                                                                                                                  188            203

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with LACY_ECOLI | P02920 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:401
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403 
           LACY_ECOLI     4 LKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPG 404
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) LacY_symp-2y5yB01 B:4-404                                                                                                                                                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) LacY_symp-2y5yB02 B:4-404                                                                                                                                                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----MFS  PDB: B:8-404 UniProt: 8-404                                                                                                                                                                                                                                                                                                                                                                              PROSITE (1)
                PROSITE (2) ------------------------------------------------------------LACY_1         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LACY_2         -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5y B   4 LKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFSFNAGCPAVEAFIEKVSRRSNFEFGRARMFGAVGWALVASIVGIMFTINNQFVFWLGSGMALILAVLLFFAKT-------VANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSSTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYITSQFEVRFSATIYLVAFAFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPG 404
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     |   -   |   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403 
                                                                                                                                                                                                                   189     197

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 '\|'

(no "SCOP Domain" information available for 2Y5Y)

(no "CATH Domain" information available for 2Y5Y)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MFS (8)

Family: LacY_symp (4)

Escherichia coli (strain K12) (4)

1a	LacY_symp-2y5yB01	B:4-404
1b	LacY_symp-2y5yB02	B:4-404

Asymmetric Unit(hide GO term definitions)

Chain A,B (LACY_ECOLI | P02920)

molecular function
	GO:0030395	lactose binding	Interacting selectively and non-covalently with lactose, a disaccharide of glucose and galactose, the carbohydrate of milk.
	GO:0015528	lactose:proton symporter activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: lactose(out) + H+(out) = lactose(in) + H+(in).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005351	sugar:proton symporter activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sugar(out) + H+(out) = sugar(in) + H+(in).
	GO:0015293	symporter activity	Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
biological process
	GO:0008643	carbohydrate transport	The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
	GO:0015767	lactose transport	The directed movement of lactose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lactose is a disaccharide 4-O-beta-D-galactopyranosyl-D-glucose, and constitutes roughly 5% of the milk in almost all mammals.
	GO:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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: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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Biological Unit
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	LACY_ECOLI \| P02920	:	1m2u 1pv6 1pv7 2cfp 2cfq 2v8n 4zyr 5gxb

1pv6	CRYSTAL STRUCTURE OF LACTOSE PERMEASE
1pv7	CRYSTAL STRUCTURE OF LACTOSE PERMEASE WITH TDG
2cfp	SUGAR FREE LACTOSE PERMEASE AT ACIDIC PH
2cfq	SUGAR FREE LACTOSE PERMEASE AT NEUTRAL PH
2v8n	WILD-TYPE STRUCTURE OF LACTOSE PERMEASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (3, 6)

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