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(-) Description

Title :  SIRC, PRECORRIN-2 DEHYDROGENASE
 
Authors :  H. L. Schubert, C. P. Hill, M. J. Warren
Date :  12 Jun 08  (Deposition) - 21 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nad Dehydrogenase, Cobalamin Biosynthesis, Nad, Oxidoreductase, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Schubert, R. S. Rose, H. K. Leech, A. A. Brindley, C. P. Hill, S. E. J. Rigby, M. J. Warren
Structure And Function Of Sirc From Bacillus Megaterium: A Metal-Binding Precorrin-2 Dehydrogenase
Biochem. J. V. 415 257 2008
PubMed-ID: 18588505  |  Reference-DOI: 10.1042/BJ20080785

(-) Compounds

Molecule 1 - PRECORRIN-2 DEHYDROGENASE
    Chains: A, B
    EC Number: 1.3.1.76
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)CODON* RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SIRC
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Synonym: SIRC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:125 , ASP A:126 , GLY A:127 , SER A:129 , PRO A:130 , THR A:133 , HOH A:216BINDING SITE FOR RESIDUE SO4 A 203
2AC2SOFTWAREGLY A:10 , ARG A:11 , SER A:12 , ASN A:70 , PHE A:72BINDING SITE FOR RESIDUE SO4 A 204
3AC3SOFTWAREILE A:21 , ARG A:24 , ARG A:25 , HOH A:262BINDING SITE FOR RESIDUE SO4 A 205
4AC4SOFTWARELEU B:186 , SER B:187 , LEU B:188 , VAL B:189BINDING SITE FOR RESIDUE SO4 B 203
5AC5SOFTWARELEU A:186 , SER A:187 , LEU A:188 , VAL A:189 , HOH A:208BINDING SITE FOR RESIDUE SO4 A 206
6AC6SOFTWAREHIS A:163 , ARG A:164 , HOH A:271 , PHE B:103BINDING SITE FOR RESIDUE SO4 A 207
7AC7SOFTWAREHOH A:211 , ARG B:11 , SER B:12 , ASN B:70 , VAL B:160 , ARG B:164BINDING SITE FOR RESIDUE GOL B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DFZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:102 -Phe B:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DFZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DFZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3DFZ)

(-) 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
(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:196
 aligned with SIRC_BACME | P61818 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           SIRC_BACME     1 MYTVMLDLKGRSVLVVGGGTIATRRIKGFLQEGAAITVVAPTVSAEINEWEAKGQLRVKRKKVGEEDLLNVFFIVVATNDQAVNKFVKQHIKNDQLVNMASSFSDGNIQIPAQFSRGRLSLAISTDGASPLLTKRIKEDLSSNYDESYTQYTQFLYECRVLIHRLNVSKSRKHELLTEIIDDQYRLSLVKQREFLQQIEKY 201
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee..hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eee....hhhhh....eeee....hhhhhhhhhhh....eee.-----...ee..eeeee..eeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfz A   1 MYTVMLDLKGRSVLVVGGGTIATRRIKGFLQEGAAITVVAPTVSAEINEWEAKGQLRVKRKKVGEEDLLNVFFIVVATNDQAVNKFVKQHIKNDQLVNM-----DGNIQIPAQFSRGRLSLAISTDGASPLLTKRIKEDLSSNYDESYTQYTQFLYECRVLIHRLNVSKSRKHELLTEIIDDQYRLSLVKQREFLQQIEKY 201
                                    10        20        30        40        50        60        70        80        90        |-    |  110       120       130       140       150       160       170       180       190       200 
                                                                                                                             99   105                                                                                                


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with SIRC_BACME | P61818 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           SIRC_BACME     1 MYTVMLDLKGRSVLVVGGGTIATRRIKGFLQEGAAITVVAPTVSAEINEWEAKGQLRVKRKKVGEEDLLNVFFIVVATNDQAVNKFVKQHIKNDQLVNMASSFSDGNIQIPAQFSRGRLSLAISTDGASPLLTKRIKEDLSSNYDESYTQYTQFLYECRVLIHRLNVSKSRKHELLTEIIDDQYRLSLVKQREFLQQIEKY 201
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee..hhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeee....hhhhhh...eeee...hhhhhhhhh--.....eeee........ee..eeeee..eeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfz B   1 MYTVMLDLKGRSVLVVGGGTIATRRIKGFLQEGAAITVVAPTVSAEINEWEAKGQLRVKRKKVGEEDLLNVFFIVVATNDQAVNKFVK--IKNDQLVNMASSFSDGNIQIPAQFSRGRLSLAISTDGASPLLTKRIKEDLSSNYDESYTQYTQFLYECRVLIHRLNVSKSRKHELLTEIIDDQYRLSLVKQREFLQQIEKY 201
                                    10        20        30        40        50        60        70        80       | -|      100       110       120       130       140       150       160       170       180       190       200 
                                                                                                                  88 91
   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  (0, 0)

(no "SCOP Domain" information available for 3DFZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DFZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DFZ)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SIRC_BACME | P61818)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0043115    precorrin-2 dehydrogenase activity    Catalysis of the reaction: NAD(+) + precorrin-2 = 2 H(+) + NADH + sirohydrochlorin.
biological process
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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.
    GO:0019354    siroheme biosynthetic process    The chemical reactions and pathways resulting in the formation of siroheme, a tetrahydroporphyrin with adjacent, reduced pyrrole rings.

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