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Title :   CRYSTALLOGRAPHIC ANALYSIS OF BETA-AXIAL LIGAND SUBSTITUTIONS IN COBALAMIN BOUND TO TRANSCOBALAMIN

Authors :   J. Wuerges, S. Geremia, L. Randaccio

Date :   19 Jun 07 (Deposition) - 30 Oct 07 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A

Keywords :   Ion Transport, Vitamin B12 Transport Protein, Transport Protein, Beta Ligand Substitution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wuerges, S. Geremia, S. N. Fedosov, L. Randaccio
Vitamin B12 Transport Proteins: Crystallographic Analysis Of Beta-Axial Ligand Substitutions In Cobalamin Bound To Transcobalamin.
Iubmb Life V. 59 722 2007
PubMed-ID: 17943552 | Reference-DOI: 10.1080/15216540701673413

Molecule 1 - TRANSCOBALAMIN-2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZ(ALPHA)-LB
	Expression System Strain	:	SMD 1168
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Organ	:	BLOOD
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	TCII, TC II, TRANSCOBALAMIN II

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	B12	1	Ligand/Ion	COBALAMIN
2	CL	3	Ligand/Ion	CHLORIDE ION
3	SO3	1	Ligand/Ion	SULFITE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:85 , GLN A:86 , THR A:134 , TYR A:137 , GLN A:138 , ASP A:179 , ASN A:227 , TYR A:229 , SER A:230 , MET A:273 , GLN A:276 , SER A:362 , LEU A:363 , SER A:364 , GLY A:365 , PRO A:366 , PHE A:367 , LEU A:368 , PHE A:381 , TRP A:382 , GLN A:383 , VAL A:384 , LEU A:392 , GLN A:393 , GLY A:395 , TRP A:414 , CL A:1416 , SO3 A:1419 , HOH A:2056 , HOH A:2090 , HOH A:2116 , HOH A:2117 , HOH A:2118 , HOH A:2119 , HOH A:2120	BINDING SITE FOR RESIDUE B12 A1415
2	AC2	SOFTWARE	TYR A:229 , THR A:267 , GLN A:269 , ASN A:270 , GLN A:394 , B12 A:1415	BINDING SITE FOR RESIDUE CL A1416
3	AC3	SOFTWARE	ARG A:356 , PHE A:357 , ARG A:358 , SER A:370 , GLY A:373	BINDING SITE FOR RESIDUE CL A1417
4	AC4	SOFTWARE	ARG A:108 , GLN A:112	BINDING SITE FOR RESIDUE CL A1418
5	AC5	SOFTWARE	B12 A:1415	BINDING SITE FOR RESIDUE SO3 A1419

Asymmetric/Biological Unit

No.	Residues
1	A:3	-	A:252
2	A:98	-	A:294
3	A:147	-	A:190

Asymmetric/Biological Unit

No.	Residues
1	Ser A:327	-	Pro A:328
2	Asp A:387	-	Pro A:388

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TCO2_BOVIN_001 *	Q	47	P	TCO2_BOVIN	---	---	A	Q	29	P
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COBALAMIN_BINDING	PS00468	Eukaryotic cobalamin-binding proteins signature.	TCO2_BOVIN	195-208	1	A:177-190

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSBTAT00000029446	1a	ENSBTAE00000240311	chr17:73063952-73064468	517	TCO2_BOVIN	1-22	22	1	A:1-4	4
1.2	ENSBTAT00000029446	2	ENSBTAE00000240310	chr17:73067760-73067952	193	TCO2_BOVIN	22-86	65	1	A:4-68	65
1.3	ENSBTAT00000029446	3	ENSBTAE00000029032	chr17:73068679-73068848	170	TCO2_BOVIN	86-143	58	1	A:68-125	58
1.4	ENSBTAT00000029446	4	ENSBTAE00000029042	chr17:73071499-73071660	162	TCO2_BOVIN	143-197	55	1	A:125-179 (gaps)	55
1.5a	ENSBTAT00000029446	5a	ENSBTAE00000408560	chr17:73072795-73072970	176	TCO2_BOVIN	197-255	59	1	A:179-237	59
1.6b	ENSBTAT00000029446	6b	ENSBTAE00000240308	chr17:73073094-73073280	187	TCO2_BOVIN	256-318	63	1	A:238-300	63
1.7	ENSBTAT00000029446	7	ENSBTAE00000398838	chr17:73074713-73074884	172	TCO2_BOVIN	318-375	58	1	A:300-357	58
1.8	ENSBTAT00000029446	8	ENSBTAE00000408006	chr17:73077140-73077255	116	TCO2_BOVIN	375-414	40	1	A:357-396	40
1.9	ENSBTAT00000029446	9	ENSBTAE00000385103	chr17:73079390-73079935	546	TCO2_BOVIN	414-433	20	1	A:396-414	19

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:405
 aligned with TCO2_BOVIN | Q9XSC9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:414
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428    
           TCO2_BOVIN    19 NICEITEVDSTLVERLGQRLLPWMDRLSQEQLNPSIYVGLRLSSLQAGAKEAHYLHSLKLSYQQSLLRPASNKDDNDSEAKPSMGQLALYLLALRANCEFIGGRKGDRLVSQLKRFLEDEKRAIGHNHQGHPRTSYYQYSLGILALCVHQKRVHDSVVGKLLYAVEHKPHLLQDHVSVDTMAMAGMAFSCLELSNLNPKQRNRINLALKRVQEKILKAQTPEGYFGNVYSTPLALQLLMGSLRPSVELGTACLKAKAALQASLQHKTFQNPLMISQLLPVLNQKSYVDLISPDCQAPRALLEPALETPPQAKVPKFIDVLLKVSGISPSYRHSVSVPAGSSLEDILKNAQEHGRFRFRTQASLSGPFLTSVLGRKAGEREFWQVLRDPDTPLQQGIADYRPKDGETIELRLVGW 432
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....hhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhh.......................eeeeeeeee......eeeeeeeee..hhhhhhhhhhhh...eeeeeee..eeeeeee..eee...eeeeeee...eee............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COBALAMIN_BIND-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a---------------------------------------------------------------Exon 1.3  PDB: A:68-125 UniProt: 86-143                   -----------------------------------------------------Exon 1.5a  PDB: A:179-237 UniProt: 197-255                 Exon 1.6b  PDB: A:238-300 UniProt: 256-318                     --------------------------------------------------------Exon 1.8  PDB: A:357-396                ------------------ Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:4-68 UniProt: 22-86                             --------------------------------------------------------Exon 1.4  PDB: A:125-179 (gaps) UniProt: 143-197       ------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:300-357 UniProt: 318-375                 --------------------------------------Exon 1.9            Transcript 1 (2)
                 2v3p A   1 NICEITEVDSTLVERLGQRLLPWMDRLSQEQLNPSIYVGLRLSSLQAGAKEAHYLHSLKLSYQQSLLRPASNKDDNDSEAKPSMGQLALYLLALRANCEFIGGRKGDRLVSQLKRFLEDEKRAIGHNHQGHPRTSYYQYSLGILALCVHQKRVHDSVVGKLLYAVEH---------SVDTMAMAGMAFSCLELSNLNPKQRNRINLALKRVQEKILKAQTPEGYFGNVYSTPLALQLLMGSLRPSVELGTACLKAKAALQASLQHKTFQNPLMISQLLPVLNQKSYVDLISPDCQAPRALLEPALETPPQAKVPKFIDVLLKVSGISPSYRHSVSVPAGSSLEDILKNAQEHGRFRFRTQASLSGPFLTSVLGRKAGEREFWQVLRDPDTPLQQGIADYRPKDGETIELRLVGW 414
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      |  -      |180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410    
                                                                                                                                                                                                167       177

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 2V3P)

(no "CATH Domain" information available for 2V3P)

(no "Pfam Domain" information available for 2V3P)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TCO2_BOVIN | Q9XSC9)

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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0006824	cobalt ion transport	The directed movement of cobalt (Co) ions 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: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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:387 - Pro A:388	[ RasMol ]
		Ser A:327 - Pro A:328	[ RasMol ]

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	TCO2_BOVIN \| Q9XSC9	:	2bb6 2bbc 2v3n

2bb6	STRUCTURE OF COBALAMIN-COMPLEXED BOVINE TRANSCOBALAMIN IN MONOCLINIC CRYSTAL FORM
2bbc	STRUCTURE OF COBALAMIN-COMPLEXED BOVINE TRANSCOBALAMIN IN TRIGONAL CRYSTAL FORM
2v3n	CRYSTALLOGRAPHIC ANALYSIS OF UPPER AXIAL LIGAND SUBSTITUTIONS IN COBALAMIN BOUND TO TRANSCOBALAMIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (9, 9)

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