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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE NICOTINATE-NUCLEOTIDE-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE FROM METHANOCALDOCOCCUS JANNASCHII DSM 2661
 
Authors :  B. Nocek, C. Hatzos, S. Clancy, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  10 Dec 09  (Deposition) - 26 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A  (2x)
Biol. Unit 5:  B (1x),C (1x)
Keywords :  Putative Nicotinate-Nucleotide-Dimethylbenzimidazole Phosphoribosyltransferase, Cobt, Mcsg, Psi, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, C. Hatzos, S. Clancy, A. Joachimiak
Crystal Structure Of A Putative Nicotinate-Nucleotide-Dimethylbenzimidazole Phosphoribosyltransferase From Methanocaldococcus Jannaschi Dsm 2661
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE NICOTINATE-NUCLEOTIDE-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MJ1598
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Synonym: UPF0284 PROTEIN MJ1598

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): A  
Biological Unit 5 (1x):  B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric Unit (2, 25)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE
2PO47Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 4 (2, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 5 (2, 9)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:38 , GLY A:39 , PRO A:153 , GLY A:154 , GLY A:155 , THR A:156 , GLY A:177BINDING SITE FOR RESIDUE PO4 A 351
2AC2SOFTWARELYS A:91 , ARG A:230 , LYS A:232 , ASN B:231BINDING SITE FOR RESIDUE PO4 A 352
3AC3SOFTWARESER B:38 , GLY B:39 , GLY B:154 , GLY B:155 , THR B:156BINDING SITE FOR RESIDUE PO4 B 351
4AC4SOFTWAREASN A:231 , ASP B:142 , ARG B:230 , LYS B:232 , LYS C:91BINDING SITE FOR RESIDUE PO4 B 352
5AC5SOFTWARELYS B:91 , ASP C:142 , ARG C:230 , ASN C:231 , LYS C:232 , PO4 C:352BINDING SITE FOR RESIDUE PO4 B 353
6AC6SOFTWARESER C:38 , GLY C:39 , PRO C:153 , GLY C:154 , GLY C:155 , THR C:156BINDING SITE FOR RESIDUE PO4 C 351
7AC7SOFTWAREPO4 B:353 , ASP C:142 , LYS C:232BINDING SITE FOR RESIDUE PO4 C 352

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L0Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:153 -Gly B:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3L0Z)

(-) 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:346
 aligned with Y1598_METJA | Q58993 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
          Y1598_METJA     1 MSIIAINENGFLDKIKGRNPLFTCVISSIETTLSIPISGVHRDVIKYTPSADVELVFYGKSLTLKTPPIDATGSPTPATITRACVELKNIKNLHIDAGAFVKPKIPFIEIDEKPTGRIEEGKAMNNSKELYMKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKVSSGSINNPHELKIKVVREGLKKAGINEKSSVFDVLNAVGDKMMPVVAGLAISFAERNKPVILAGGTQMSAVLAVIKEINKKVLDKNLIAIGTTEFVLNDKKGDLKGIVEQIGNVPVLASKFYFEKAKIEGLKNYCKGSVKEGVGAGGIAVYSIVNDLEPTKIREFIENKFYE 346
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhh....eeeeeee...hhhhh......hhhhhhhhhhhhhhhhhhh..........hhhhh..hhhhhhhhhhhhh.....eee..........eeee.....hhhhh....hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhh...eeee..hhhhh.hhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0z A   1 mSIIAINENGFLDKIKGRNPLFTCVISSIETTLSIPISGVHRDVIKYTPSADVELVFYGKSLTLKTPPIDATGSPTPATITRACVELKNIKNLHIDAGAFVKPKIPFIEIDEKPTGRIEEGKAmNNSKELYmKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKVSSGSINNPHELKIKVVREGLKKAGINEKSSVFDVLNAVGDKmmPVVAGLAISFAERNKPVILAGGTQmSAVLAVIKEINKKVLDKNLIAIGTTEFVLNDKKGDLKGIVEQIGNVPVLASKFYFEKAKIEGLKNYCKGSVKEGVGAGGIAVYSIVNDLEPTKIREFIENKFYE 346
                            |       10        20        30        40        50        60        70        80        90       100       110       120   |   130 |     140       150       160       170       180       190       200       210     ||220       230       240 |     250       260       270       280       290       300       310       320       330       340      
                            |                                                                                                                        124-MSE 132-MSE                                                                             216-MSE                   242-MSE                                                                                                    
                            1-MSE                                                                                                                                                                                                                 217-MSE                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with Y1598_METJA | Q58993 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
          Y1598_METJA     1 MSIIAINENGFLDKIKGRNPLFTCVISSIETTLSIPISGVHRDVIKYTPSADVELVFYGKSLTLKTPPIDATGSPTPATITRACVELKNIKNLHIDAGAFVKPKIPFIEIDEKPTGRIEEGKAMNNSKELYMKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKVSSGSINNPHELKIKVVREGLKKAGINEKSSVFDVLNAVGDKMMPVVAGLAISFAERNKPVILAGGTQMSAVLAVIKEINKKVLDKNLIAIGTTEFVLNDKKGDLKGIVEQIGNVPVLASKFYFEKAKIEGLKNYCKGSVKEGVGAGGIAVYSIVNDLEPTKIREFIENKFYE 346
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhh...eeeeeee...hhhhh............hhhhhhhhhhhh.................hhhhhhhhhhhhh......ee...........ee.......hhhhh....hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh........----...hhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhh...hhhhhhhhhh...eeee........hhhhhh..........hhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0z B   1 mSIIAINENGFLDKIKGRNPLFTCVISSIETTLSIPISGVHRDVIKYTPSADVELVFYGKSLTLKTPPIDATGSPTPATITRACVELKNIKNLHIDAGAFVKPKIPFIEIDEKPTGRIEEGKAmNNSKELYmKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKV----INNPHELKIKVVREGLKKAGINEKSSVFDVLNAVGDKmmPVVAGLAISFAERNKPVILAGGTQmSAVLAVIKEINKKVLDKNLIAIGTTEFVLNDKKGDLKGIVEQIGNVPVLASKFYFEKAKIEGLKNYCKGSVKEGVGAGGIAVYSIVNDLEPTKIREFIENKFYE 346
                            |       10        20        30        40        50        60        70        80        90       100       110       120   |   130 |     140       150       160       170   |   180       190       200       210     ||220       230       240 |     250       260       270       280       290       300       310       320       330       340      
                            1-MSE                                                                                                                    124-MSE 132-MSE                                   174  179                                  216-MSE                   242-MSE                                                                                                    
                                                                                                                                                                                                                                                  217-MSE                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:340
 aligned with Y1598_METJA | Q58993 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:345
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340     
          Y1598_METJA     1 MSIIAINENGFLDKIKGRNPLFTCVISSIETTLSIPISGVHRDVIKYTPSADVELVFYGKSLTLKTPPIDATGSPTPATITRACVELKNIKNLHIDAGAFVKPKIPFIEIDEKPTGRIEEGKAMNNSKELYMKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKVSSGSINNPHELKIKVVREGLKKAGINEKSSVFDVLNAVGDKMMPVVAGLAISFAERNKPVILAGGTQMSAVLAVIKEINKKVLDKNLIAIGTTEFVLNDKKGDLKGIVEQIGNVPVLASKFYFEKAKIEGLKNYCKGSVKEGVGAGGIAVYSIVNDLEPTKIREFIENKFY 345
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------DBI_PRT-3l0zC01 C:69-285                                                                                                                                                                                                 ------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------DBI_PRT-3l0zC02 C:69-285                                                                                                                                                                                                 ------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------DBI_PRT-3l0zC03 C:69-285                                                                                                                                                                                                 ------------------------------------------------------------ Pfam domains (3)
         Sec.struct. author ..eeee...hhhhhhh...eeeeeee..hhhhhh............hhhhhhhhhhhhh................hhhhhhhhhhhhh......ee...........ee.......hhhhh....hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh........-----..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh........eeeeeehhhhh....hhhhhhhhhh...eeee..hhhhh.................hhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0z C   1 mSIIAINENGFLDKIKGRNPLFTCVISSIETTLSIPISGVHRDVIKYTPSADVELVFYGKSLTLKTPPIDATGSPTPATITRACVELKNIKNLHIDAGAFVKPKIPFIEIDEKPTGRIEEGKAmNNSKELYmKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKV-----NNPHELKIKVVREGLKKAGINEKSSVFDVLNAVGDKmmPVVAGLAISFAERNKPVILAGGTQmSAVLAVIKEINKKVLDKNLIAIGTTEFVLNDKKGDLKGIVEQIGNVPVLASKFYFEKAKIEGLKNYCKGSVKEGVGAGGIAVYSIVNDLEPTKIREFIENKFY 345
                            |       10        20        30        40        50        60        70        80        90       100       110       120   |   130 |     140       150       160       170   |   180       190       200       210     ||220       230       240 |     250       260       270       280       290       300       310       320       330       340     
                            1-MSE                                                                                                                    124-MSE 132-MSE                                   174   180                                 216-MSE                   242-MSE                                                                                                   
                                                                                                                                                                                                                                                  217-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 3L0Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L0Z)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: DBI_PRT] (24)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Y1598_METJA | Q58993)
molecular function
    GO:0008939    nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity    Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate.
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.

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