1N4A - JenaLib

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

Authors :   N. K. Karpowich, P. C. Smith, J. F. Hunt, Northeast Structural Genomi Consortium (Nesg)

Date :   30 Oct 02 (Deposition) - 11 Mar 03 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Abc Transporter, Periplasmic Binding Protein, Vitamin B12, Transmembrane Transport, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, 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

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 (2, 6)

No.	Name	Count	Type	Full Name
1	CNC	2	Ligand/Ion	CO-CYANOCOBALAMIN
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CNC	1	Ligand/Ion	CO-CYANOCOBALAMIN
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CNC	1	Ligand/Ion	CO-CYANOCOBALAMIN
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:9 , ALA A:10 , TYR A:28 , TRP A:44 , TRP A:63 , GLY A:65 , GLY A:66 , PHE A:146 , TRP A:174 , SER A:219 , ASP A:220 , GLU A:223 , ARG A:224 , HOH A:7034 , HOH A:7035 , HOH A:7046 , HOH A:7048 , HOH A:7069 , HOH A:7115 , HOH A:7143 , HOH A:7167 , HOH A:7179 , HOH A:7187 , HOH A:7203 , HOH A:7225 , HOH A:7250 , HOH A:7325 , HOH A:7376 , HOH A:7431 , HOH A:7436 , HOH A:7497 , HOH A:7503 , HOH A:7540	BINDING SITE FOR RESIDUE CNC A 501
2	AC2	SOFTWARE	PRO B:5009 , ALA B:5010 , SER B:5027 , TYR B:5028 , TRP B:5044 , TRP B:5063 , GLY B:5065 , GLY B:5066 , TRP B:5174 , SER B:5219 , ASP B:5220 , GLU B:5223 , ARG B:5224 , HOH B:7010 , HOH B:7083 , HOH B:7109 , HOH B:7141 , HOH B:7475 , HOH B:7520	BINDING SITE FOR RESIDUE CNC B 5501

Asymmetric Unit

No.	Residues
1	A:161	-	A:237
2	B:5161	-	B:5237

Asymmetric Unit

No.	Residues
1	Tyr A:31	-	Pro A:32
2	Asn A:143	-	Pro A:144
3	Pro A:144	-	Pro A:145
4	Tyr B:5031	-	Pro B:5032
5	Asn B:5143	-	Pro B:5144
6	Pro B:5144	-	Pro B:5145

(no "SAP(SNP)/Variant" information available for 1N4A)

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:5003-5244

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:5003-5244

(no "Exon" information available for 1N4A)

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
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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 d1n4aa_ A: Vitamin B12 binding protein BtuF                                                                                                                                                                                                          SCOP domains
               CATH domains 1n4aA01 A:1-118 Nitrogenase molybdenum iron protein domain                                                            1n4aA02 A:119-244 Nitrogenase molybdenum iron protein domain                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhh......ee.....hhhhhhh.eee.....hhhhhhhh...eeeee....hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhh.eee............hhhhhhhh...eeee..hhhhhhhhhhhhhhhh...eee.hhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FE_B12_PBP  PDB: A:3-244 UniProt: 25-266                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1n4a 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: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 d1n4ab_ B: Vitamin B12 binding protein BtuF                                                                                                                                                                                                          SCOP domains
               CATH domains 1n4aB01 B:5001-5118 Nitrogenase molybdenum iron protein domain                                                        1n4aB02 B:5119-5244 Nitrogenase molybdenum iron protein domain                                                                 CATH domains
           Pfam domains (1) ---Peripla_BP_2-1n4aB01 B:5004-5209                                                                                                                                                                              ----------------------------------- Pfam domains (1)
           Pfam domains (2) ---Peripla_BP_2-1n4aB02 B:5004-5209                                                                                                                                                                              ----------------------------------- Pfam domains (2)
         Sec.struct. author ...eee.hhhhhhhhhhh......ee.....hhhhhhh.eeee..eehhhhhhhh...eeeee....hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhh.eee............hhhhhhhh...eeee..hhhhhhhhhhhhh......eee.hhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FE_B12_PBP  PDB: B:5003-5244 UniProt: 25-266                                                                                                                                                                                                       PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1n4a B 5001 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGmNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVmWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD 5244
                                  5010      5020      5030      5040      5050      5060      5070      5080  |   5090      5100      5110      5120      5130      5140      5150      5160      5170      5180      5190      5200      5210      5220      5230      5240    
                                                                       5047-MSE                            5083-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(

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Folds(

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Superfamilies( (-)

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Families(

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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	d1n4aa_	A:
1b	d1n4ab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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	1n4aA02	A:119-244
1b	1n4aB02	B:5119-5244
1c	1n4aA01	A:1-118
1d	1n4aB01	B:5001-5118

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_2-1n4aB01	B:5004-5209
1b	Peripla_BP_2-1n4aB02	B:5004-5209

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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	BTUF_ECOLI \| P37028	:	1n2z 1n4d 2qi9 4dbl 4fi3 5m29 5m2q 5m34 5m3b

1bmt	METHIONINE SYNTHASE
1efd	FHUD BOUND TO GALLICHROME
1n4d	RELATED ID: EC1 RELATED DB: TARGETDB

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