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(-) Description

Title :  COBALT CHELATASE CBIK (PERIPLASMATIC) FROM DESULVOBRIO VULGARIS HILDENBOROUGH (CO-CRYSTALLIZED WITH COBALT)
 
Authors :  C. V. Romao, S. A. L. Lobo, M. A. Carrondo, L. M. Saraiva, P. M. Matias
Date :  28 Oct 10  (Deposition) - 22 Dec 10  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. V. Romao, D. Ladakis, S. A. L. 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 - CHELATASE, PUTATIVE
    Chains: A
    EC Number: 4.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 GOLD (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-28
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 29-297
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH
    Synonym: COBALT CHELATASE CBIK

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 16)

Asymmetric Unit (7, 16)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CO1Ligand/IonCOBALT (II) ION
3GOL3Ligand/IonGLYCEROL
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5NA1Ligand/IonSODIUM ION
6PER1Ligand/IonPEROXIDE ION
7SO48Ligand/IonSULFATE ION
Biological Unit 1 (4, 52)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CO-1Ligand/IonCOBALT (II) ION
3GOL12Ligand/IonGLYCEROL
4HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5NA-1Ligand/IonSODIUM ION
6PER4Ligand/IonPEROXIDE ION
7SO432Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:91 , HIS A:96 , LEU A:99 , LEU A:119 , PRO A:159 , HOH A:2040 , HOH A:2105BINDING SITE FOR RESIDUE HEM A1270
02AC2SOFTWAREHIS A:154 , GLU A:184 , HIS A:216 , PER A:1285 , HOH A:2106BINDING SITE FOR RESIDUE CO A1271
03AC3SOFTWAREGLY A:92 , GLU A:93 , GLU A:94 , THR A:156 , HIS A:158 , HOH A:2037 , HOH A:2055 , HOH A:2107BINDING SITE FOR RESIDUE SO4 A1272
04AC4SOFTWAREPHE A:17 , LEU A:87 , HIS A:88 , THR A:89 , MET A:210 , ALA A:211 , NA A:1283 , HOH A:2108BINDING SITE FOR RESIDUE SO4 A1273
05AC5SOFTWAREARG A:114 , VAL A:115 , SER A:116 , VAL A:117 , ARG A:267BINDING SITE FOR RESIDUE SO4 A1274
06AC6SOFTWARELEU A:174 , ASP A:175 , ASP A:197 , ARG A:236 , HOH A:2065BINDING SITE FOR RESIDUE GOL A1275
07AC7SOFTWARETRP A:172 , PRO A:176 , ARG A:199BINDING SITE FOR RESIDUE GOL A1276
08AC8SOFTWARETHR A:49 , LYS A:51 , MET A:52 , GLU A:94BINDING SITE FOR RESIDUE GOL A1277
09AC9SOFTWAREPRO A:140 , ALA A:141 , HOH A:2109BINDING SITE FOR RESIDUE SO4 A1278
10BC1SOFTWARESER A:250 , ASP A:251 , ALA A:252BINDING SITE FOR RESIDUE SO4 A1279
11BC2SOFTWARETHR A:19 , SER A:20 , VAL A:21 , ASP A:215 , SO4 A:1281 , HOH A:2110BINDING SITE FOR RESIDUE SO4 A1280
12BC3SOFTWAREGLY A:214 , ASP A:215 , HIS A:216 , SO4 A:1280 , HOH A:2106 , HOH A:2110 , HOH A:2111BINDING SITE FOR RESIDUE SO4 A1281
13BC4SOFTWAREPRO A:43 , VAL A:44 , ARG A:45 , HOH A:2112BINDING SITE FOR RESIDUE SO4 A1282
14BC5SOFTWAREGLY A:153 , HIS A:154 , TYR A:164 , SO4 A:1273BINDING SITE FOR RESIDUE NA A1283
15BC6SOFTWAREHIS A:154 , GLU A:184 , HIS A:216 , CO A:1271BINDING SITE FOR RESIDUE PER A1285

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:186 -Pro A:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XVZ)

(-) 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:263
 aligned with CBIKP_DESVH | Q72EC8 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:263
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   
          CBIKP_DESVH    35 AQKTGILLVAFGTSVEEARPALDKMGDRVRAAHPDIPVRWAYTAKMIRAKLRAEGIAAPSPAEALAGMAEEGFTHVAVQSLHTIPGEEFHGLLETAHAFQGLPKGLTRVSVGLPLIGTTADAEAVAEALVASLPADRKPGEPVVFMGHGTPHPADICYPGLQYYLWRLDPDLLVGTVEGSPSFDNVMAELDVRKAKRVWLMPLMAVAGDHARNDMAGDEDDSWTSQLARRGIEAKPVLHGTAESDAVAAIWLRHLDDALARLN 297
               SCOP domains d2xvza_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---CbiK-2xvzA01 A:10-266                                                                                                                                                                                                                                            --- Pfam domains
         Sec.struct. author ...eeeeeee........hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh.....hhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh...eeeeee.....hhhhhhh.......hhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xvz A   7 AQKTGILLVAFGTSVEEARPALDKMGDRVRAAHPDIPVRWAYTAKMIRAKLRAEGIAAPSPAEALAGMAEEGFTHVAVQSLHTIPGEEFHGLLETAHAFQGLPKGLTRVSVGLPLIGTTADAEAVAEALVASLPADRKPGEPVVFMGHGTPHPADICYPGLQYYLWRLDPDLLVGTVEGSPSFDNVMAELDVRKAKRVWLMPLMAVAGDHARNDMAGDEDDSWTSQLARRGIEAKPVLHGTAESDAVAAIWLRHLDDALARLN 269
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
   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)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Chelatase (20)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (CBIKP_DESVH | Q72EC8)
molecular function
    GO:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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:0051266    sirohydrochlorin ferrochelatase activity    Catalysis of the reaction: siroheme + 2 H+ = Fe(2+) + sirohydrochlorin.
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:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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        CBIKP_DESVH | Q72EC8: 2xvx 2xvy

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