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(-) Description

Title :  ANAEROBIC COBALT CHELATASE FROM ARCHEAOGLOBUS FULGIDUS ( CBIX) IN COMPLEX WITH METALATED SIROHYDROCHLORIN PRODUCT
 
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 :  2.01
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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

(-) Compounds

Molecule 1 - SIROHYDROCHLORIN COBALTOCHELATASE
    Chains: A, B, C, D
    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: PET3A
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: CBIXS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SIR2Ligand/IonCOBALT SIROHYDROCHLORIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SIR1Ligand/IonCOBALT SIROHYDROCHLORIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SIR1Ligand/IonCOBALT SIROHYDROCHLORIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:10 , GLY A:11 , SER A:12 , GLN A:13 , ARG A:44 , ARG A:46 , PHE A:68 , ILE A:69 , SER A:70 , GLY A:72 , LEU A:73 , HIS A:74 , HOH A:2005 , HOH A:2025 , HIS B:10 , GLY B:11 , SER B:12 , ARG B:44 , ARG B:46 , PHE B:68 , ILE B:69 , SER B:70 , GLY B:72 , LEU B:73 , HIS B:74 , HOH B:2056 , HOH B:2057 , HOH B:2058 , HOH B:2059BINDING SITE FOR RESIDUE SIR B1126
2AC2SOFTWAREHIS C:10 , SER C:12 , GLN C:13 , TYR C:17 , ARG C:44 , ARG C:46 , ARG C:47 , ARG C:55 , PHE C:68 , ILE C:69 , SER C:70 , GLY C:72 , LEU C:73 , HIS C:74 , HIS D:10 , SER D:12 , TYR D:17 , ARG D:44 , ARG D:46 , PHE D:68 , ILE D:69 , SER D:70 , GLY D:72 , LEU D:73 , HIS D:74 , HOH D:2047 , HOH D:2048 , HOH D:2049BINDING SITE FOR RESIDUE SIR D1126

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Arg A:47 -Pro A:48
2Arg B:47 -Pro B:48
3Gly C:11 -Ser C:12
4Arg C:47 -Pro C:48
5Arg D:47 -Pro D:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XWQ)

(-) Sequences/Alignments

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 d2xwqa_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhh....eeeeee.....hhhhhhhhhhhh........eeeee..eeeee......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xwq 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 d2xwqb_ B: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhh...eeeeee.....hhhhhhhhhhhhh.......eeeee..eeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwq B   1 MRRGLVIVGHGSQLNHYREVMELHRKRIEESGAFDEVKIAFAARKRRPMPDEAIREMNCDIIYVVPLFISYGLHVTEDLPDLLGFPRGRGIKEGEFEGKKVVICEPIGEDYFVTYAILNSVFRIG 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain C 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 d2xwqc_ C: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhh....eeeeeee....hhhhhhhhhhhh...........ee..eeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xwq C   0 GMRRGLVIVGHGSQLNHYREVMELHRKRIEESGAFDEVKIAFAARKRRPMPDEAIREMNCDIIYVVPLFISYGLHVTEDLPDLLGFPRGRGIKEGEFEGKKVVICEPIGEDYFVTYAILNSVFRIG 125
                                     9        19        29        39        49        59        69        79        89        99       109       119      


Chain D 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 d2xwqd_ D: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------CbiX-2xwqD01 D:10-119                                                                                         ------ Pfam domains (1)
           Pfam domains (2) ---------CbiX-2xwqD02 D:10-119                                                                                         ------ Pfam domains (2)
           Pfam domains (3) ---------CbiX-2xwqD03 D:10-119                                                                                         ------ Pfam domains (3)
           Pfam domains (4) ---------CbiX-2xwqD04 D:10-119                                                                                         ------ Pfam domains (4)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhh...eeeeee.....hhhhhhhhhhhh........eeeee..eeeee......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwq D   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Chelatase (20)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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  2xwq
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  4.99.1.3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CBIX_ARCFU | O29537: 1tjn 2dj5 2xws

(-) Related Entries Specified in the PDB File

1tjn CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN AF0721 FROMARCHAEOGLOBUS FULGIDUS
2dj5 CRYSTAL STRUCTURE OF THE VITAMIN B12 BIOSYNTHETICCOBALTOCHELATASE, CBIXS, FROM ARCHAEOGLOBUS FULGIDUS
2xwp ANAEROBIC COBALT CHELATASE (CBIK) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH METALATED TETRAPYRROLE
2xws ANAEROBIC COBALT CHELATASE (CBIX) FROM SALMONELLA TYPHIMURIUM