1QGO - JenaLib

Title :   ANAEROBIC COBALT CHELATASE IN COBALAMIN BIOSYNTHESIS FROM SALMONELLA TYPHIMURIUM

Authors :   H. L. Schubert, E. Raux, M. J. Warren, K. S. Wilson

Date :   03 May 99 (Deposition) - 29 Sep 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Cobalamin, Vitamin B12, Metal Ion Chelation, Chelatase, Cobalt Precorrin, Cbik, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. L. Schubert, E. Raux, K. S. Wilson, M. J. Warren
Common Chelatase Design In The Branched Tetrapyrrole Pathways Of Heme And Anaerobic Cobalamin Synthesis.
Biochemistry V. 38 10660 1999
PubMed-ID: 10451360 | Reference-DOI: 10.1021/BI9906773
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:87 , ASP A:88 , GLU A:89 , SER A:148 , HIS A:150 , HOH A:584 , HOH A:640 , HOH A:646 , HOH A:675 , HOH A:714	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	VAL A:174 , GLU A:175 , VAL A:180 , TRP A:220 , ARG A:223 , HOH A:555 , HOH A:695 , HOH A:702	BINDING SITE FOR RESIDUE SO4 A 401
3	AC3	SOFTWARE	GLN A:64 , LYS A:221 , PRO A:233 , HOH A:568 , HOH A:667	BINDING SITE FOR RESIDUE SO4 A 402
4	CO	AUTHOR	HIS A:145 , HIS A:207	THE ACTIVE SITE IS LOCATED IN A CLEFT BETWEEN THE TWO DOMAINS SURROUNDED BY FOUR REGIONS OF STRUCTURE COMPRISED RESPECTIVELY BY RESIDUES 10-14, 86-89, 145- 149, 205-207. HIS 145 AND HIS 207 ARE THE TWO RESIDUES SHOWN TO BE RESPONSIBLE FOR METAL BINDING.

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

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
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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 d1qgoa_ A: Cobalt chelatase CbiK                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1qgoA02 A:2-113,A:237-258  [code=3.40.50.1400, no name defined]                                                 1qgoA01 A:114-236  [code=3.40.50.1400, no name defined]                                                                    1qgoA02                CATH domains
               Pfam domains -CbiK-1qgoA01 A:3-257                                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhh.hhhhhhhhhhh....eeeeee..hhhhhhhhhhh......hhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhh...eeeeee......hhhh..........hhhhhhh...eeeee...hhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qgo 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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric/Biological 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.

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