Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  PRECORRIN-8X METHYLMUTASE RELATED PROTEIN
 
Authors :  M. E. Cuff, A. Joachimiak, S. Korolev, A. Savchenko, A. Edwards, Midwest Center For Structural Genomics (Mcsg)
Date :  24 Mar 03  (Deposition) - 07 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Methylmutase, Precorrin-8X, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, D. J. Miller, S. Korolev, X. Xu, W. F. Anderson, A. Edwards, A. Joachimiak, A. Savchenko
Crystal Structure Of A Predicted Precorrin-8X Methylmutase From Thermoplasma Acidophilum.
Proteins V. 58 751 2004
PubMed-ID: 15609338  |  Reference-DOI: 10.1002/PROT.20022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRECORRIN-8X METHYLMUTASE RELATED PROTEIN
    Chains: A, B, C, D
    EC Number: 5.4.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TA0654
    Organism Scientific: THERMOPLASMA ACIDOPHILUM DSM 1728
    Organism Taxid: 273075
    Strain: DSM1728

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric/Biological Unit (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1OU0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OU0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OU0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OU0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OU0)

(-) Exons   (0, 0)

(no "Exon" information available for 1OU0)

(-) 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:190
 aligned with Q9HKE7_THEAC | Q9HKE7 from UniProtKB/TrEMBL  Length:207

    Alignment length:190
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
         Q9HKE7_THEAC    17 SLAAIDSMIDPDISGPMRHIVVKAIHAAGDFAIAPLIRYSDGFFKSMLAKLKEGCTIICDSEMVRAGIYSRPVLERNRVVCYLNDVRSKEMADVNGITRSAAGIRIAMQDHRNSVIVIGNAPTALLEAMRMIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
               SCOP domains d1ou0a_ A: Precorrin-8x methylmutase related protein                                                                                                                                           SCOP domains
               CATH domains 1ou0A00 A:17-206 Precorrin-8X methylmutase CbiC/CobH                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhh.eeee.hhhhhhhh.hhhhhhhheeee...hhhhhhhhhhhh.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ou0 A  17 SLAAIDSmIDPDISGPmRHIVVKAIHAAGDFAIAPLIRYSDGFFKSmLAKLKEGCTIICDSEmVRAGIYSRPVLERNRVVCYLNDVRSKEmADVNGITRSAAGIRIAmQDHRNSVIVIGNAPTALLEAmRmIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
                                   |26      | 36        46        56      | 66        76  |     86        96       106|      116       126       136       146|      156       166       176       186       196       206
                                  24-MSE   33-MSE                        63-MSE          79-MSE                     107-MSE          124-MSE              145-MSE                                                         
                                                                                                                                                            147-MSE                                                       


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with Q9HKE7_THEAC | Q9HKE7 from UniProtKB/TrEMBL  Length:207

    Alignment length:193
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
         Q9HKE7_THEAC    14 EERSLAAIDSMIDPDISGPMRHIVVKAIHAAGDFAIAPLIRYSDGFFKSMLAKLKEGCTIICDSEMVRAGIYSRPVLERNRVVCYLNDVRSKEMADVNGITRSAAGIRIAMQDHRNSVIVIGNAPTALLEAMRMIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
               SCOP domains d1ou0b_ B: Precorrin-8x methylmutase related protein                                                                                                                                              SCOP domains
               CATH domains 1ou0B00 B:14-206 Precorrin-8X methylmutase CbiC/CobH                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhh.eeee.hhhhhhhh.hhhhhhhheee......hhhhhhhhhh.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ou0 B  14 EERSLAAIDSmIDPDISGPmRHIVVKAIHAAGDFAIAPLIRYSDGFFKSmLAKLKEGCTIICDSEmVRAGIYSRPVLERNRVVCYLNDVRSKEmADVNGITRSAAGIRIAmQDHRNSVIVIGNAPTALLEAmRmIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
                                    23|       33        43        53        63        73     |  83        93       103   |   113       123|      133       143 | |   153       163       173       183       193       203   
                                     24-MSE   33-MSE                        63-MSE          79-MSE                     107-MSE          124-MSE              145-MSE                                                         
                                                                                                                                                               147-MSE                                                       


Chain C from PDB  Type:PROTEIN  Length:191
 aligned with Q9HKE7_THEAC | Q9HKE7 from UniProtKB/TrEMBL  Length:207

    Alignment length:191
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 
         Q9HKE7_THEAC    16 RSLAAIDSMIDPDISGPMRHIVVKAIHAAGDFAIAPLIRYSDGFFKSMLAKLKEGCTIICDSEMVRAGIYSRPVLERNRVVCYLNDVRSKEMADVNGITRSAAGIRIAMQDHRNSVIVIGNAPTALLEAMRMIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
               SCOP domains d1ou0c_ C: Precorrin-8x methylmutase related protein                                                                                                                                            SCOP domains
               CATH domains 1ou0C00 C:16-206 Precorrin-8X methylmutase CbiC/CobH                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhh.eeee.hhhhhhhh.hhhhhhhheeee...hhhhhhhhhhhh.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ou0 C  16 RSLAAIDSmIDPDISGPmRHIVVKAIHAAGDFAIAPLIRYSDGFFKSmLAKLKEGCTIICDSEmVRAGIYSRPVLERNRVVCYLNDVRSKEmADVNGITRSAAGIRIAmQDHRNSVIVIGNAPTALLEAmRmIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
                                    25       |35        45        55       |65        75   |    85        95       105 |     115       125       135       145 |     155       165       175       185       195       205 
                                   24-MSE   33-MSE                        63-MSE          79-MSE                     107-MSE          124-MSE              145-MSE                                                         
                                                                                                                                                             147-MSE                                                       


Chain D from PDB  Type:PROTEIN  Length:191
 aligned with Q9HKE7_THEAC | Q9HKE7 from UniProtKB/TrEMBL  Length:207

    Alignment length:191
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 
         Q9HKE7_THEAC    16 RSLAAIDSMIDPDISGPMRHIVVKAIHAAGDFAIAPLIRYSDGFFKSMLAKLKEGCTIICDSEMVRAGIYSRPVLERNRVVCYLNDVRSKEMADVNGITRSAAGIRIAMQDHRNSVIVIGNAPTALLEAMRMIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
               SCOP domains d1ou0d_ D: Precorrin-8x methylmutase related protein                                                                                                                                            SCOP domains
               CATH domains 1ou0D00 D:16-206 Precorrin-8X methylmutase CbiC/CobH                                                                                                                                            CATH domains
           Pfam domains (1) CbiC-1ou0D01 D:16-206                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) CbiC-1ou0D02 D:16-206                                                                                                                                                                           Pfam domains (2)
           Pfam domains (3) CbiC-1ou0D03 D:16-206                                                                                                                                                                           Pfam domains (3)
           Pfam domains (4) CbiC-1ou0D04 D:16-206                                                                                                                                                                           Pfam domains (4)
         Sec.struct. author hhhhhhh........hhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhh.eeee.hhhhhhhh.hhhhhhhheeee...hhhhhhhhhhhh.hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ou0 D  16 RSLAAIDSmIDPDISGPmRHIVVKAIHAAGDFAIAPLIRYSDGFFKSmLAKLKEGCTIICDSEmVRAGIYSRPVLERNRVVCYLNDVRSKEmADVNGITRSAAGIRIAmQDHRNSVIVIGNAPTALLEAmRmIEENGWYDIPIVGIPVGFINASKAKEGLVSSHIEYISVEGHRGGSPIAASIVNGFGRFL 206
                                    25       |35        45        55       |65        75   |    85        95       105 |     115       125       135       145 |     155       165       175       185       195       205 
                                   24-MSE   33-MSE                        63-MSE          79-MSE                     107-MSE          124-MSE              145-MSE                                                         
                                                                                                                                                             147-MSE
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CbiC] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9HKE7_THEAC | Q9HKE7)
molecular function
    GO:0016993    precorrin-8X methylmutase activity    Catalysis of the reaction: precorrin-8X = hydrogenobyrinate.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1ou0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ou0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ou0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9HKE7_THEAC | Q9HKE7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  5.4.1.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9HKE7_THEAC | Q9HKE7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1OU0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1OU0)