1UQW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YLIB PROTEIN FROM ESCHERICHIA COI

Authors :   S. Jeudy, C. Abergel, J. M. Claverie

Date :   22 Oct 03 (Deposition) - 22 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.72

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Zn Binding Protein, Transport, Lipoprotein, Bacterial Targets At Igs-Cnrs, France, Bigs, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Jeudy, C. Abergel, J. M. Claverie
Crystal Structure Of Ylib Protein From E. Coli
To Be Published
PubMed: search

Molecule 1 - PUTATIVE BINDING PROTEIN YLIB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST17
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 32)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	12	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 11)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:99	BINDING SITE FOR RESIDUE ZN A 500
02	AC2	SOFTWARE	GLU A:149 , ZN A:502 , HOH A:2146 , ASP B:168	BINDING SITE FOR RESIDUE ZN A 501
03	AC3	SOFTWARE	GLU A:149 , ZN A:501 , ASP B:168	BINDING SITE FOR RESIDUE ZN A 502
04	AC4	SOFTWARE	ASP A:168 , ZN A:504 , HOH A:2147 , HOH A:2149 , GLU B:149	BINDING SITE FOR RESIDUE ZN A 503
05	AC5	SOFTWARE	ASP A:168 , ZN A:503 , HOH A:2148 , HOH A:2149 , GLU B:149	BINDING SITE FOR RESIDUE ZN A 504
06	AC6	SOFTWARE	GLU A:214 , HOH A:2150 , HIS B:332 , HIS B:334	BINDING SITE FOR RESIDUE ZN A 505
07	AC7	SOFTWARE	GLU A:236 , MSE A:238 , HIS A:466 , ZN A:507	BINDING SITE FOR RESIDUE ZN A 506
08	AC8	SOFTWARE	GLU A:236 , HIS A:466 , ZN A:506	BINDING SITE FOR RESIDUE ZN A 507
09	AC9	SOFTWARE	ASP A:307 , ASP B:433	BINDING SITE FOR RESIDUE ZN A 508
10	BC1	SOFTWARE	HIS A:332 , HIS A:334 , HOH A:2151 , GLU B:214	BINDING SITE FOR RESIDUE ZN A 509
11	BC2	SOFTWARE	HIS B:99	BINDING SITE FOR RESIDUE ZN B 510
12	BC3	SOFTWARE	GLU B:236 , MSE B:238 , HIS B:466	BINDING SITE FOR RESIDUE ZN B 511
13	BC4	SOFTWARE	LYS A:33 , LYS A:49 , PHE A:483 , GLU A:484	BINDING SITE FOR RESIDUE GOL A 550
14	BC5	SOFTWARE	MSE A:46 , LEU A:48 , ASN A:133 , ALA A:296 , GLY A:391	BINDING SITE FOR RESIDUE GOL A 551

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

Asymmetric Unit

No.	Residues
1	Leu A:189	-	Pro A:190
2	Phe A:219	-	Pro A:220
3	Pro A:407	-	Pro A:408
4	Leu B:189	-	Pro B:190
5	Phe B:219	-	Pro B:220
6	Pro B:407	-	Pro B:408

(no "SAP(SNP)/Variant" information available for 1UQW)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	GSIB_ECOLI	76-98	2	A:53-75 B:53-75

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	GSIB_ECOLI	76-98	1	A:53-75 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	GSIB_ECOLI	76-98	1	- B:53-75

(no "Exon" information available for 1UQW)

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:487
 aligned with GSIB_ECOLI | P75797 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:487
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       
           GSIB_ECOLI    26 AAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFYPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKESGVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
               SCOP domains d1uqwa_ A: Hypothetical protein YliB                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhh.hhhhhhhhh......eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhh..hhhhh..eeeeeeee..eeeeee.....hhhhhhh.......hhhhhhhhhhhh.........eeeeeee...eeeeee.............eeeeee..hhhhhhhhhhhh...ee...hhhhhhhhhhh..eeeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....................hhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhh...........eeeeeee....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee..ee..ee.....ee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uqw A   3 AAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEmKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRHNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAmISPAALEKYGKEIGFYPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAmLQTGEAQFAFPIPYEQATLLEKNKNIELmASPSImQRYISmNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAmDAGQRAAEVEGKGQKESGVRmFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWImPDTGFSFEDADLQ 489
                                    12        22        32        42   |    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |212       222       232     | 242 |     252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472   |   482       
                                                                      46-MSE                                                                                         142-MSE                                                            209-MSE                      238-MSE |     |                                                                                                           360-MSE              381-MSE                                                                                        476-MSE         
                                                                                                                                                                                                                                                                           244-MSE |                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                 250-MSE

Chain B from PDB  Type:PROTEIN  Length:487
 aligned with GSIB_ECOLI | P75797 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:487
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       
           GSIB_ECOLI    26 AAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEMKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRYNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAMISPAALEKYGKEIGFYPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAMLQTGEAQFAFPIPYEQATLLEKNKNIELMASPSIMQRYISMNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAMDAGQRAAEVEGKGQKESGVRMFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWIMPDTGFSFEDADLQ 512
               SCOP domains d1uqwb_ B: Hypothetical protein YliB                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------SBP_bac_5-1uqwB01 B:47-408                                                                                                                                                                                                                                                                                                                                                --------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------SBP_bac_5-1uqwB02 B:47-408                                                                                                                                                                                                                                                                                                                                                --------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee.......hhhhh.hhhhhhhhh......eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhh..hhhhh..eeeeeeee..eeeeee.....hhhhhhh.......hhhhhhhhhhhh.........eeeeee.....eeeee.............eeeeee..hhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eee....................hhhhhhhhhhh..................hhhhhhhhhhhhhh...........hhhhhhhhh.......................hhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..ee..ee.....ee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uqw B   3 AAKDVVVAVGSNFTTLDPYDANDTLSQAVAKSFYQGLFGLDKEmKLKNVLAESYTVSDDGITYTVKLREGIKFQDGTDFNAAAVKANLDRASDPANHLKRHNLYKNIAKTEAIDPTTVKITLKQPFSAFINILAHPATAmISPAALEKYGKEIGFYPVGTGPYELDTWNQTDFVKVKKFAGYWQPGLPKLDSITWRPVADNNTRAAmLQTGEAQFAFPIPYEQATLLEKNKNIELmASPSImQRYISmNVTQKPFDNPKVREALNYAINRPALVKVAFAGYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKEAGYPNGFSTTLWSSHNHSTAQKVLQFTQQQLAQVGIKAQVTAmDAGQRAAEVEGKGQKESGVRmFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTNDPAEKTRLYKAAQDIIWQESPWIPLVVEKLVSAHSKNLTGFWImPDTGFSFEDADLQ 489
                                    12        22        32        42   |    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |212       222       232     | 242 |     252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472   |   482       
                                                                      46-MSE                                                                                         142-MSE                                                            209-MSE                      238-MSE |     |                                                                                                           360-MSE              381-MSE                                                                                        476-MSE         
                                                                                                                                                                                                                                                                           244-MSE |                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                 250-MSE

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: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Hypothetical protein YliB (1)

Escherichia coli [TaxId: 562] (1)

1a	d1uqwa_	A:
1b	d1uqwb_	B:

(no "CATH Domain" information available for 1UQW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_5 (33)

Escherichia coli (strain K12) (12)

1a	SBP_bac_5-1uqwB01	B:47-408
1b	SBP_bac_5-1uqwB02	B:47-408

Asymmetric Unit(hide GO term definitions)

Chain A,B (GSIB_ECOLI | P75797)

molecular function
	GO:0034634	glutathione transmembrane transporter activity	Enables the directed movement of glutathione, the tripeptide glutamylcysteinylglycine, across a membrane into, out of or within a cell, or between cells.
biological process
	GO:0006974	cellular response to DNA damage stimulus	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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0034775	glutathione transmembrane transport	A process in which glutathione is transported from one side of a membrane to the other 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:0043190	ATP-binding cassette (ABC) transporter complex	A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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	Cis Peptide Bonds
		Leu A:189 - Pro A:190	[ RasMol ]
		Leu B:189 - Pro B:190	[ RasMol ]
		Phe A:219 - Pro A:220	[ RasMol ]
		Phe B:219 - Pro B:220	[ RasMol ]
		Pro A:407 - Pro A:408	[ RasMol ]
		Pro B:407 - Pro B:408	[ RasMol ]

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	1uqw
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Description

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Ligands, Modified Residues, Ions (3, 32)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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