2DJ5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE VITAMIN B12 BIOSYNTHETIC COBALTOCHELATASE, CBIXS, FROM ARCHAEOGLOBUS FULGIDUS

Authors :   J. Yin, M. M. Cherney, M. N. G. James

Date :   31 Mar 06 (Deposition) - 12 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Beta-Alpha-Beta, Parallel Beta Sheet, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Yin, L. X. Xu, M. M. Cherney, E. Raux-Deery, A. A. Bindley, A. Savchenko, J. R. Walker, M. E. Cuff, M. J. Warren, M. N. G. James
Crystal Structure Of The Vitamin B(12) Biosynthetic Cobaltochelatase, Cbix (S), From Archaeoglobus Fulgidus
J. Struct. Funct. Genom. V. 7 37 2006
PubMed-ID: 16835730 | Reference-DOI: 10.1007/S10969-006-9008-X

Molecule 1 - SIROHYDROCHLORIN COBALTOCHELATASE
	Chains	:	A, B
	EC Number	:	4.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3) STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CBIX
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	CBIXS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	PO4	8	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:0 , MET A:1 , ARG A:2 , ASP A:35	BINDING SITE FOR RESIDUE PO4 A 133
2	AC2	SOFTWARE	TYR A:111 , LEU B:23 , ARG B:27	BINDING SITE FOR RESIDUE PO4 B 133
3	AC3	SOFTWARE	LEU A:23 , ARG A:27 , TYR B:111	BINDING SITE FOR RESIDUE PO4 B 134
4	AC4	SOFTWARE	TYR A:17 , PHE B:68 , ILE B:69 , SER B:70 , HOH B:148 , HOH B:156	BINDING SITE FOR RESIDUE PO4 B 135
5	AC5	SOFTWARE	GLY A:0 , ARG A:2 , GOL A:203 , HOH A:204 , ASP B:60	BINDING SITE FOR RESIDUE GOL A 201
6	AC6	SOFTWARE	ILE A:69 , SER A:70 , HOH B:156	BINDING SITE FOR RESIDUE GOL A 202
7	AC7	SOFTWARE	GOL A:201 , MET B:1 , ARG B:2	BINDING SITE FOR RESIDUE GOL A 203

(no "SS Bond" information available for 2DJ5)

Asymmetric Unit

No.	Residues
1	Arg A:47	-	Pro A:48
2	Arg B:47	-	Pro B:48

(no "SAP(SNP)/Variant" information available for 2DJ5)

(no "PROSITE Motif" information available for 2DJ5)

(no "Exon" information available for 2DJ5)

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:126
 aligned with CBIX_ARCFU | O29537 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:126
                             1                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119      
           CBIX_ARCFU     - -MRRGLVIVGHGSQLNHYREVMELHRKRIEESGAFDEVKIAFAARKRRPMPDEAIREMNCDIIYVVPLFISYGLHVTEDLPDLLGFPRGRGIKEGEFEGKKVVICEPIGEDYFVTYAILNSVFRIG 125
               SCOP domains d2dj5a_ A: automated matches                                                                                                   SCOP domains
               CATH domains 2dj5A00 A:0-125  [code=3.40.50.1400, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhh....eeeeee.....hhhhhhhhhhh.........eeeee..eeeee......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dj5 A   0 GMRRGLVIVGHGSQLNHYREVMELHRKRIEESGAFDEVKIAFAARKRRPMPDEAIREMNCDIIYVVPLFISYGLHVTEDLPDLLGFPRGRGIKEGEFEGKKVVICEPIGEDYFVTYAILNSVFRIG 125
                                     9        19        29        39        49        59        69        79        89        99       109       119

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with CBIX_ARCFU | O29537 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           CBIX_ARCFU     1 MRRGLVIVGHGSQLNHYREVMELHRKRIEESGAFDEVKIAFAARKRRPMPDEAIREMNCDIIYVVPLFISYGLHVTEDLPDLLGFPRGRGIKEGEFEGKKVVICEPIGEDYFVTYAILNSVFRIG 125
               SCOP domains d2dj5b_ B: automated matches                                                                                                  SCOP domains
               CATH domains 2dj5B00 B:1-125  [code=3.40.50.1400, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhh....eeeeee.....hhhhhhhhhhh.........eeeee..eeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dj5 B   1 MRRGLVIVGHGSQLNHYREVMELHRKRIEESGAFDEVKIAFAARKRRPMPDEAIREMNCDIIYVVPLFISYGLHVTEDLPDLLGFPRGRGIKEGEFEGKKVVICEPIGEDYFVTYAILNSVFRIG 125
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: Chelatase-like (149)

Superfamily: Chelatase (46)

Family: CbiX-like (4)

Protein domain: automated matches (3)

Archaeoglobus fulgidus [TaxId: 2234] (3)

1a	d2dj5a_	A:
1b	d2dj5b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1400, no name defined] (36)

Archaeoglobus fulgidus. Organism_taxid: 2234. (2)

1a	2dj5A00	A:0-125
1b	2dj5B00	B:1-125

(no "Pfam Domain" information available for 2DJ5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CBIX_ARCFU | O29537)

molecular function
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016852	sirohydrochlorin cobaltochelatase activity	Catalysis of the reaction: sirohydrochlorin + Co2+ = cobalt-sirohydrochlorin + 2 H+.
	GO:0046906	tetrapyrrole binding	Interacting selectively and non-covalently with a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position.
biological process
	GO:0019251	anaerobic cobalamin biosynthetic process	The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the absence of oxygen.
	GO:0009236	cobalamin biosynthetic process	The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:47 - Pro A:48	[ RasMol ]
		Arg B:47 - Pro B:48	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	2dj5
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	4.99.1.3
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UniProtKB/Swiss-Prot
	CBIX_ARCFU \| O29537	:	1tjn 2xwq 2xws

1tjn	THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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