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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE COBALAMIN SYNTHESIS RELATED PROTEIN (COBF) FROM CORYNEBACTERIUM DIPHTHERIAE
 
Authors :  B. Nocek, M. Zhou, S. Clancy, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)
Date :  27 Oct 06  (Deposition) - 28 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Cobalamin Synthesis Related Protein, Cobf, Psi-2, Mad, Structural Genomics, Sam, S-Adenosylmethionine, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, M. Zhou, S. Clancy, A. Joachimiak
Crystal Structure Of Cobalamin Synthesis Related Protein (Cobf) From Corynebacterium Diphtheriae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE COBALAMIN SYNTHESIS RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
4SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (3, 14)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
4SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:218 , LEU A:249BINDING SITE FOR RESIDUE MG A 251
2AC2SOFTWARETHR A:11 , TRP A:109 , GLY A:110 , ASP A:111 , LEU A:114 , TYR A:115 , THR A:142 , ALA A:143 , MSE A:184 , LEU A:185 , PHE A:206 , LEU A:207 , MSE A:241 , ASP A:242 , THR A:243 , HOH A:4640 , HOH A:4659 , HOH A:4675 , HOH A:4691 , HOH A:4720 , HOH A:4781 , HOH A:4822BINDING SITE FOR RESIDUE SAM A 4633
3AC3SOFTWARETYR A:115 , ASP A:116 , SER A:117 , ARG A:120 , ASN A:156 , ILE A:158 , GLY A:159BINDING SITE FOR RESIDUE GOL A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NPN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NPN)

(-) 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:238
 aligned with Q6NIF5_CORDI | Q6NIF5 from UniProtKB/TrEMBL  Length:250

    Alignment length:251
                             1                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
         Q6NIF5_CORDI     - -MRTIYVIGIGTGSPEFLTLQAISGLRHAQAIVALDKGEQKSDLLALRQKIVDTHAPGTPIYAVTDPERDRNPDNYEEEVRRWHAERAHLLASTIRERTPDDGAVAFLVWGDPSLYDSTLRIIEHMRNLEDLHADVKVIPGITAVQVLTAEHGILINRIGEAIHITTGRNLPETSAKDRRNCVVMLDGKTAWQDVATEHTYMWWGAFLGTEQQVLRKGYVHEIGAQVAELKQQLRTEHGWIMDTYLLRELD 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2npnA01 A:0-141 Cobalt-precorrin-4 T   ransmethylase; Domain 1                                                                                2npnA02 A:142-250 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                              CATH domains
               Pfam domains ---TP_methylase-2npnA01 A:3-223                                                                                                                                                                                                 --------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.eeeee.---.hhhhhhhhhhhhhhhh....eeee..----------hhhhhhhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhh..........eeee..hhhhh..hhh.eeeee.....hhhhhh...eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2npn A   0 AmRTIYVIGIGTGSPEFLTLQAISGLRHAQAIVALD---QKSDLLALRQKIVDTHAPGTPIYAVTD----------EEEVRRWHAERAHLLASTIRERTPDDGAVAFLVWGDPSLYDSTLRIIEHmRNLEDLHADVKVIPGITAVQVLTAEHGILINRIGEAIHITTGRNLPETSAKDRRNCVVmLDGKTAWQDVATEHTYmWWGAFLGTEQQVLRKGYVHEIGAQVAELKQQLRTEHGWImDTYLLRELD 250
                             |       9        19        29     |  39        49        59     |   -      | 79        89        99       109       119     | 129       139       149       159       169       179    |  189       199 |     209       219       229       239 |     249 
                             |                                35  39                        65         76                                              125-MSE                                                    184-MSE          201-MSE                                 241-MSE     
                             1-MSE
   Legend:   → Mismatch (orange background)
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  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 2NPN)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: TP_methylase] (35)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q6NIF5_CORDI | Q6NIF5)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0043819    precorrin-6A synthase (deacetylating) activity    Catalysis of the reaction: S-adenosyl-L-methionine + H(2)O + precorrin-5 = S-adenosyl-L-homocysteine + acetate + 2 H(+) + precorrin-6X.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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