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(-) Description

Title :  CRYSTAL STRUCTURE OF MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOG FROM SHEWANELLA ONEIDENSIS
 
Authors :  C. Chang, L. Bigelow, A. Joachimiak, Midwest Center For Structural (Mcsg)
Date :  08 Oct 09  (Deposition) - 20 Oct 09  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Structural Genomics, Molybdenum Cofactor Biosynthesis Protein Mog, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, L. Bigelow, A. Joachimiak
Crystal Structure Of Molybdenum Cofactor Biosynthesis Protein Mog From Shewanella Oneidensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOG
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG
    Expression System Strain: BL21(DE3) DERIVATIVE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MOG, SO_0065
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 34)

Asymmetric Unit (2, 34)
No.NameCountTypeFull Name
1MSE31Mod. Amino AcidSELENOMETHIONINE
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:62 , ASP A:126 , SER A:127 , HOH A:248 , HOH A:276 , HOH A:303BINDING SITE FOR RESIDUE NA A 178
2AC2SOFTWAREALA D:62 , ARG D:124 , ASP D:126 , SER D:127 , HOH D:181 , HOH D:248 , HOH D:283BINDING SITE FOR RESIDUE NA D 178
3AC3SOFTWAREALA E:62 , ASP E:126 , SER E:127 , HOH E:234 , HOH E:324BINDING SITE FOR RESIDUE NA E 178

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K6A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K6A)

(-) Exons   (0, 0)

(no "Exon" information available for 3K6A)

(-) 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:176
 aligned with Q8EKM7_SHEON | Q8EKM7 from UniProtKB/TrEMBL  Length:177

    Alignment length:176
                             1                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169      
         Q8EKM7_SHEON     - -MSKAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRMMPGFGELMRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLMEGPYLECNEAVIKPFRPK 175
               SCOP domains d3k6aa_ A: MogA                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..........hhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6a A   0 AmSKAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKmADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRmmPGFGELmRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLmEGPYLECNEAVIKPFRPK 175
                             |       9        19        29        39        49        59 |      69        79        89     || 99   |   109       119       129       139       149       159       169      
                             |                                                          61-MSE                            95-MSE   |                                                   157-MSE              
                             1-MSE                                                                                         96-MSE  |                                                                        
                                                                                                                                 103-MSE                                                                    


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q8EKM7_SHEON | Q8EKM7 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q8EKM7_SHEON     3 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRMMPGFGELMRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLMEGPYLECNEAVIKPFRP 174
               SCOP domains d3k6ab_ B: MogA                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhh..hhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh...hhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6a B   3 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKmADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRmmPGFGELmRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLmEGPYLECNEAVIKPFRP 174
                                    12        22        32        42        52        62        72        82        92  ||   102|      112       122       132       142       152    |  162       172  
                                                                                     61-MSE                            95-MSE   |                                                   157-MSE             
                                                                                                                        96-MSE  |                                                                       
                                                                                                                              103-MSE                                                                   


Chain C from PDB  Type:PROTEIN  Length:173
 aligned with Q8EKM7_SHEON | Q8EKM7 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171   
         Q8EKM7_SHEON     2 SKAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRMMPGFGELMRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLMEGPYLECNEAVIKPFRP 174
               SCOP domains d3k6ac_ C: MogA                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhh...hhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6a C   2 SKAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKmADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRmmPGFGELmRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLmEGPYLECNEAVIKPFRP 174
                                    11        21        31        41        51        61        71        81        91   ||  101 |     111       121       131       141       151     | 161       171   
                                                                                      61-MSE                            95-MSE   |                                                   157-MSE             
                                                                                                                         96-MSE  |                                                                       
                                                                                                                               103-MSE                                                                   


Chain D from PDB  Type:PROTEIN  Length:172
 aligned with Q8EKM7_SHEON | Q8EKM7 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q8EKM7_SHEON     3 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRMMPGFGELMRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLMEGPYLECNEAVIKPFRP 174
               SCOP domains d3k6ad_ D: MogA                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..........hhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6a D   3 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKmADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRmmPGFGELmRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLmEGPYLECNEAVIKPFRP 174
                                    12        22        32        42        52        62        72        82        92  ||   102|      112       122       132       142       152    |  162       172  
                                                                                     61-MSE                            95-MSE   |                                                   157-MSE             
                                                                                                                        96-MSE  |                                                                       
                                                                                                                              103-MSE                                                                   


Chain E from PDB  Type:PROTEIN  Length:171
 aligned with Q8EKM7_SHEON | Q8EKM7 from UniProtKB/TrEMBL  Length:177

    Alignment length:171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
         Q8EKM7_SHEON     3 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRMMPGFGELMRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLMEGPYLECNEAVIKPFR 173
               SCOP domains d3k6ae_ E: MogA                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh...hhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6a E   3 KAKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKmADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRmmPGFGELmRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLmEGPYLECNEAVIKPFR 173
                                    12        22        32        42        52        62        72        82        92  ||   102|      112       122       132       142       152    |  162       172 
                                                                                     61-MSE                            95-MSE   |                                                   157-MSE            
                                                                                                                        96-MSE  |                                                                      
                                                                                                                              103-MSE                                                                  


Chain F from PDB  Type:PROTEIN  Length:170
 aligned with Q8EKM7_SHEON | Q8EKM7 from UniProtKB/TrEMBL  Length:177

    Alignment length:170
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
         Q8EKM7_SHEON     4 AKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKMADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRMMPGFGELMRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLMEGPYLECNEAVIKPFR 173
               SCOP domains d3k6af_ F: MogA                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---MoCF_biosynth-3k6aF01 F:7-152                                                                                                                     --------------------- Pfam domains (1)
           Pfam domains (2) ---MoCF_biosynth-3k6aF02 F:7-152                                                                                                                     --------------------- Pfam domains (2)
           Pfam domains (3) ---MoCF_biosynth-3k6aF03 F:7-152                                                                                                                     --------------------- Pfam domains (3)
           Pfam domains (4) ---MoCF_biosynth-3k6aF04 F:7-152                                                                                                                     --------------------- Pfam domains (4)
           Pfam domains (5) ---MoCF_biosynth-3k6aF05 F:7-152                                                                                                                     --------------------- Pfam domains (5)
           Pfam domains (6) ---MoCF_biosynth-3k6aF06 F:7-152                                                                                                                     --------------------- Pfam domains (6)
         Sec.struct. author .eeeeeeehhhhhhhh..hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6a F   4 AKIGIVTVSDRASAGIYEDISGKAIIDTLNDYLTSEWEPIYQVIPDEQDVIETTLIKmADEQDCCLIVTTGGTGPAKRDVTPEATEAVCDRmmPGFGELmRAESLKFVPTAILSRQTAGLRGDSLIVNLPGKPKSIRECLDAVFPAIPYCIDLmEGPYLECNEAVIKPFR 173
                                    13        23        33        43        53       |63        73        83        93 ||    103       113       123       133       143       153   |   163       173
                                                                                    61-MSE                            95-MSE   |                                                   157-MSE            
                                                                                                                       96-MSE  |                                                                      
                                                                                                                             103-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 6)

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

(-) CATH Domains  (0, 0 ; only for superseded entry 2FUW: 1,6)

(no "CATH Domain" information available for 3K6A, only for superseded entry 2FUW replaced by 3K6A)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: MoCF_biosynth] (31)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q8EKM7_SHEON | Q8EKM7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006777    Mo-molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
    GO:0032324    molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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        Q8EKM7_SHEON | Q8EKM7: 2f7w 2f7y 4nwo

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