2XWP - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   ANAEROBIC COBALT CHELATASE (CBIK) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH METALATED TETRAPYRROLE

Authors :   D. Ladakis, A. A. Brindley, E. Deery, M. J. Warren, R. W. Pickersgill

Date :   04 Nov 10 (Deposition) - 22 Dec 10 (Release) - 26 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

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

Reference :   C. V. Romao, D. Ladakis, S. A. Lobo, M. A. Carrondo, A. A. Brindley, E. Deery, P. M. Matias, R. W. Pickersgill, L. M. Saraiva, M. J. Warren
Evolution In A Family Of Chelatases Facilitated By The Introduction Of Active Site Asymmetry And Protein Oligomerization.
Proc. Natl. Acad. Sci. Usa V. 108 97 2011
PubMed-ID: 21173279 | Reference-DOI: 10.1073/PNAS.1014298108

Molecule 1 - SIROHYDROCHLORIN COBALTOCHELATASE
	Chains	:	A
	EC Number	:	4.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 STAR DE3
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector	:	PET 14B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SALMONELLA ENTERICA
	Organism Taxid	:	90371
	Variant	:	SEROVAR TYPHIMURIUM

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SIR	1	Ligand/Ion	COBALT SIROHYDROCHLORIN

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	SIR	6	Ligand/Ion	COBALT SIROHYDROCHLORIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:10 , THR A:43 , SER A:44 , GLY A:45 , MET A:46 , ALA A:71 , GLN A:72 , GLY A:73 , HIS A:83 , ILE A:84 , ILE A:85 , GLY A:87 , ASP A:88 , GLU A:89 , LYS A:92 , HIS A:145 , GLY A:146 , ALA A:147 , MET A:201 , LEU A:202 , VAL A:203 , HIS A:207 , ALA A:208 , HOH A:2061 , HOH A:2139 , HOH A:2140 , HOH A:2141 , HOH A:2142 , HOH A:2143	BINDING SITE FOR RESIDUE SIR A1259
2	AC2	SOFTWARE	ARG A:52 , LYS A:68 , GLN A:72 , HOH A:2144 , HOH A:2145	BINDING SITE FOR RESIDUE GOL A1260

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

Asymmetric Unit

No.	Residues
1	Tyr A:177	-	Pro A:178

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

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

(no "Exon" information available for 2XWP)

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:257
 aligned with CBIK_SALTY | Q05592 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           CBIK_SALTY     2 KKALLVVSFGTSYHDTCEKNIVACERDLAASCPDRDLFRAFTSGMIIRKLRQRDGIDIDTPLQALQKLAAQGYQDVAIQSLHIINGDEYEKIVREVQLLRPLFTRLTLGVPLLSSHNDYVQLMQALRQQMPSLRQTEKVVFMGHGASHHAFAAYACLDHMMTAQRFPARVGAVESYPEVDILIDSLRDEGVTGVHLMPLMLVAGDHAINDMASDDGDSWKMRFNAAGIPATPWLSGLGENPAIRAMFVAHLHQALNM 258
               SCOP domains d2xwpa_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -CbiK-2xwpA01 A:3-257                                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhh........eeeeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh....hhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwp A   2 KKALLVVSFGTSYHDTCEKNIVACERDLAASCPDRDLFRAFTSGMIIRKLRQRDGIDIDTPLQALQKLAAQGYQDVAIQSLHIINGDEYEKIVREVQLLRPLFTRLTLGVPLLSSHNDYVQLMQALRQQMPSLRQTEKVVFMGHGASHHAFAAYACLDHMMTAQRFPARVGAVESYPEVDILIDSLRDEGVTGVHLMPLMLVAGDHAINDMASDDGDSWKMRFNAAGIPATPWLSGLGENPAIRAMFVAHLHQALNM 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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: Cobalt chelatase CbiK (2)

Protein domain: automated matches (1)

Salmonella typhimurium [TaxId: 90371] (1)

d2xwpa_

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Chelatase (20)

Family: CbiK (4)

Salmonella typhimurium (2)

CbiK-2xwpA01

A:3-257

Asymmetric Unit(hide GO term definitions)

Chain A (CBIK_SALTY | Q05592)

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.
	GO:0006779	porphyrin-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		SIR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:177 - Pro A:178	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2xwp
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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	CBIK_SALTY \| Q05592
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	4.99.1.3
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	CBIK_SALTY \| Q05592
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UniProtKB/Swiss-Prot
	CBIK_SALTY \| Q05592	:	1qgo

1qgo	ANAEROBIC COBALT CHELATASE IN COBALAMIN BIOSYNTHESIS FROM SALMONELLA TYPHIMURIUM
2xwq	ANAEROBIC COBALT CHELATASE FROM ARCHEAOGLOBUS FULGIDUS (CBIX) IN COMPLEX WITH METALATED SIROHYDROCHLORIN PRODUCT
2xws	ANAEROBIC COBALT CHELATASE (CBIX) FROM SALMONELLA TYPHIMURIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

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Related Entries

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