1NQF - JenaLib

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Title :   OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHIONINE SUBSTIUTION CONSTRUCT FOR SE-MET SAD PHASING

Authors :   D. P. Chimento, A. K. Mohanty, R. J. Kadner, M. C. Wiener

Date :   21 Jan 03 (Deposition) - 29 Apr 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A

Keywords :   Beta Barrel, Cobalamin, Vitamin B12, Outer Membrane Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. P. Chimento, A. K. Mohanty, R. J. Kadner, M. C. Wiener
Substrate-Induced Transmembrane Signaling In The Cobalamin Transporter Btub
Nat. Struct. Biol. V. 10 394 2003
PubMed-ID: 12652322 | Reference-DOI: 10.1038/NSB914
(for further references see the PDB file header)

Molecule 1 - VITAMIN B12 RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BTUB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	OUTER MEMBRANE COBALAMIN TRANSPORTER BTUB

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	C8E	6	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:174 , HIS A:176 , HIS A:449	BINDING SITE FOR RESIDUE MG A 806
2	AC2	SOFTWARE	ARG A:358 , SER A:359 , ARG A:367 , GLY A:369 , THR A:370 , PHE A:470 , ASP A:471 , THR A:472 , GLY A:473 , C8E A:805 , HOH A:832	BINDING SITE FOR RESIDUE C8E A 800
3	AC3	SOFTWARE	MSE A:317 , THR A:338 , ASP A:361 , ASN A:362 , SER A:363 , PHE A:379 , TYR A:383 , PHE A:422	BINDING SITE FOR RESIDUE C8E A 801
4	AC4	SOFTWARE	TRP A:300 , ASN A:302 , VAL A:304 , ALA A:313 , VAL A:315 , TRP A:431 , TYR A:481	BINDING SITE FOR RESIDUE C8E A 802
5	AC5	SOFTWARE	ILE A:311 , LEU A:342 , GLY A:344 , THR A:373 , C8E A:805	BINDING SITE FOR RESIDUE C8E A 803
6	AC6	SOFTWARE	SER A:434 , GLY A:435 , TYR A:436 , ARG A:437 , LYS A:462 , GLY A:463 , VAL A:464	BINDING SITE FOR RESIDUE C8E A 804
7	AC7	SOFTWARE	ALA A:357 , TRP A:371 , GLY A:473 , HIS A:477 , C8E A:800 , C8E A:803 , HOH A:832	BINDING SITE FOR RESIDUE C8E A 805

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:82	-	Val A:83
2	Gly A:89	-	Val A:90
3	Ser A:91	-	Gly A:92
4	Gln A:159	-	Leu A:160
5	Gly A:406	-	Asn A:407
6	Tyr A:534	-	Pro A:535

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TONB_DEPENDENT_REC_2	PS01156	TonB-dependent receptor proteins signature 2.	BTUB_ECOLI	597-614	1	A:577-594

(no "Exon" information available for 1NQF)

Asymmetric/Biological 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:544
 aligned with BTUB_ECOLI | P06129 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:588
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606        
           BTUB_ECOLI    27 TLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 614
               SCOP domains d1nqfa_ A: Outer membrane cobalamin transporter BtuB                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1nqfA01 A:7-130 Ferric Hydroxamate Uptake Protein; Chain A, domain 1                                                        1nqfA02 A:131-594  [code=2.40.170.20, no name                    defined]                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -----------Plug-1nqfA02 A:18-126                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TonB_dep_Rec-1nqfA01 A:370-593                                                                                                                                                                                                  - Pfam domains
         Sec.struct. author .ee.......ee.hhh...eeeeehhhhhhhh.............eeeee.......eeeee........eeee...................hhhhh.eeeeee..hhhhhh.....eeeeee......eeeeeeeee....eeeeeeeee.....eeeeeeeeeee..-------------------.eeeeeeeeeeeee....eeeeeeeeeeeeee.------------..eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee.----------.eeeeeeeeeeeeeeeee...eeeeeeeeeeeeee.....---..eeeeeeeeeeeeeee...eeeeeeeeeeee...eeeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhh.........eeeeeeeeeeeeee..eeeeeeeeeeeee..eee......eee...eeeeeeeeeeeee...eeeeeeeeeeeeee............eeeeeeeeee....eeeeeeeee..eeeee......eeeee..eeeeeeeeeee.....eeeeee....................eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TONB_DEPENDENT_REC PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nqf A   7 TLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTH-------------------GFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTN------------DTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNY----------ATLDEmKQYTVQWANNVIVGHGSIGAGVDmQmQmTTPGTG---DGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDmGmTmQYLGTRYDKDYSSYPYQTVKmGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 594
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176         -       196       206       216       226 |       -    |  246       256       266       276|        - |    |296       306       316| | |  326|   |  336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516 | |   526       536    |  546       556       566       576       586        
                                                                                                                                                                                                   176                 196                             228          241                                 277        288    |                     317-MSE   327 331                                                                                                                                                                                      516-MSE                  541-MSE                                                 
                                                                                                                                                                                                                                                                                                                        293-MSE                   319-MSE                                                                                                                                                                                                518-MSE                                                                        
                                                                                                                                                                                                                                                                                                                                                    321-MSE                                                                                                                                                                                                520-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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Transmembrane beta-barrels (143)

Superfamily: Porins (99)

Family: Ligand-gated protein channel (29)

Protein domain: Outer membrane cobalamin transporter BtuB (12)

Escherichia coli [TaxId: 562] (12)

d1nqfa_

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MBB (97)

Family: TonB_dep_Rec (26)

Escherichia coli (strain K12) (16)

TonB_dep_Rec-1nqfA01

A:370-593

Clan: Ubiquitin (279)

Family: Plug (26)

Escherichia coli (strain K12) (16)

Plug-1nqfA02

A:18-126

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (BTUB_ECOLI | P06129)

molecular function
	GO:0015235	cobalamin transporter activity	Enables the directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0015889	cobalamin transport	The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules 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:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	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:0046930	pore complex	Any small opening in a membrane that allows the passage of gases and/or liquids.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gln A:159 - Leu A:160	[ RasMol ]
		Gly A:406 - Asn A:407	[ RasMol ]
		Gly A:82 - Val A:83	[ RasMol ]
		Gly A:89 - Val A:90	[ RasMol ]
		Ser A:91 - Gly A:92	[ RasMol ]
		Tyr A:534 - Pro A:535	[ RasMol ]

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	1nqf
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	BTUB_ECOLI \| P06129	:	1nqe 1nqg 1nqh 1ujw 2gsk 2guf 2ysu 3m8b 3m8d 3rgm 3rgn

1nqe	OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI
1nqg	OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM
1nqh	OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM AND CYANOCOBALAMIN (VITAMIN B12) SUBSTRATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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