1N4D - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE LIGAND-FREE STRUCTURE OF E COLI BTUF, THE PERIPLASMIC BINDING PROTEIN FOR VITAMIN B12

Authors :   N. Karpowich, P. C. Smith, J. F. Hunt

Date :   30 Oct 02 (Deposition) - 11 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Abc Transporter, Vitamin B12, Periplasmic Binding Protein, Transmembrane Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Karpowich, H. H. Huang, P. C. Smith, J. F. Hunt
Crystal Structures Of The Btuf Periplasmic-Binding Protein For Vitamin B12 Suggest A Functionally Important Reduction In Protein Mobility Upon Ligand Binding
J. Biol. Chem. V. 278 8429 2003
PubMed-ID: 12468528 | Reference-DOI: 10.1074/JBC.M212239200
(for further references see the PDB file header)

Molecule 1 - VITAMIN B12 TRANSPORT PROTEIN BTUF
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		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 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1N4D)

Asymmetric Unit

No.	Residues
1	A:161	-	A:237
2	B:1161	-	B:1237

Asymmetric Unit

No.	Residues
1	Tyr A:31	-	Pro A:32
2	Asn A:143	-	Pro A:144
3	Tyr B:1031	-	Pro B:1032
4	Asn B:1143	-	Pro B:1144

(no "SAP(SNP)/Variant" information available for 1N4D)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	BTUF_ECOLI	25-266	2	A:3-244 B:1003-1244

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	BTUF_ECOLI	25-266	1	A:3-244 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	BTUF_ECOLI	25-266	1	- B:1003-1244

(no "Exon" information available for 1N4D)

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:244
 aligned with BTUF_ECOLI | P37028 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
          BTUF_ECOLI     23 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD  266
               SCOP domains d1n4da_ A: Vitamin B12 binding protein BtuF                                                                                                                                                                                                          SCOP domains
               CATH domains 1n4dA01 A:1-118 Nitrogenase molybdenum iron protein domain                                                            1n4dA02 A:119-244 Nitrogenase molybdenum iron protein domain                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhh.....ee......hhhhhhh.........hhhhhhhhh..eeeehhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....eeeee.............hhhhhhhhhh.eee.hhhh.......hhhhhhhh....eee.....................eee.hhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FE_B12_PBP  PDB: A:3-244 UniProt: 25-266                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1n4d A    1 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGmNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVmWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD  244
                                    10        20        30        40      | 50        60        70        80  |     90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
                                                                         47-MSE                              83-MSE

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with BTUF_ECOLI | P37028 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
          BTUF_ECOLI     23 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD  266
               SCOP domains d1n4db_ B: Vitamin B12 binding protein BtuF                                                                                                                                                                                                          SCOP domains
               CATH domains 1n4dB01 B:1001-1118 Nitrogenase molybdenum iron protein domain                                                        1n4dB02 B:1119-1244 Nitrogenase molybdenum iron protein domain                                                                 CATH domains
           Pfam domains (1) ---Peripla_BP_2-1n4dB01 B:1004-1194                                                                                                                                                               -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Peripla_BP_2-1n4dB02 B:1004-1194                                                                                                                                                               -------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eee.hhhhhhhhhhh.............hhhhhhh.........hhhhhhhhh..eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh........eeeee.............hhhhhhhhhh.eee..............hhhhhhh...eee..-----------------..eee.hhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FE_B12_PBP  PDB: B:1003-1244 UniProt: 25-266                                                                                                                                                                                                       PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1n4d B 1001 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGmNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVmWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITG-----------------IPVIPLTSDWFERASPRIILAAQQLCNALSQVD 1244
                                  1010      1020      1030      1040      1050      1060      1070      1080  |   1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190   |     -         - |    1220      1230      1240    
                                                                       1047-MSE                            1083-MSE                                                                                                       1194              1212

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: TroA-like (17)

Protein domain: Vitamin B12 binding protein BtuF (4)

Escherichia coli [TaxId: 562] (4)

1a	d1n4da_	A:
1b	d1n4db_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)

Escherichia coli. Organism_taxid: 562. (5)

1a	1n4dA02	A:119-244
1b	1n4dB02	B:1119-1244
1c	1n4dA01	A:1-118
1d	1n4dB01	B:1001-1118

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Peripla_BP_2] (13)

Family: Peripla_BP_2 (13)

Escherichia coli (strain K12) (5)

1a	Peripla_BP_2-1n4dB01	B:1004-1194
1b	Peripla_BP_2-1n4dB02	B:1004-1194

Asymmetric Unit(hide GO term definitions)

Chain A,B (BTUF_ECOLI | P37028)

molecular function
	GO:0031419	cobalamin binding	Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
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: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: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
		Asn A:143 - Pro A:144	[ RasMol ]
		Asn B:1143 - Pro B:1144	[ RasMol ]
		Tyr A:31 - Pro A:32	[ RasMol ]
		Tyr B:1031 - Pro B:1032	[ RasMol ]

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