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(-) Description

Title :  STRUCTURE OF THE ARCHAEAL GTP:ADOCBI-P GUANYLYLTRANSFERASE (COBY) FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  S. A. Newmister, M. M. Otte, J. C. Escalante-Semerena, I. Rayment
Date :  02 May 11  (Deposition) - 18 May 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Pyrophosphorylase Binding Motif, Pyrophosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Newmister, M. M. Otte, J. C. Escalante-Semerena, I. Rayment
Structure And Mutational Analysis Of The Archaeal Gtp:Adocbi-P Guanylyltransferase (Coby) From Methanocaldococcus Jannaschii: Insights Into Gtp Binding An Dimerization.
Biochemistry V. 50 5301 2011
PubMed-ID: 21542645  |  Reference-DOI: 10.1021/BI200329T

(-) Compounds

Molecule 1 - ADENOSYLCOBINAMIDE-PHOSPHATE GUANYLYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOBY14
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: COBY, MJ1117
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: ADOCBI-P GUANYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 7)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:6 , ALA A:7 , THR A:12 , ARG A:13 , LYS A:19 , SER A:50 , GLU A:82 , SER A:99 , SER A:100 , ASN A:179 , HOH A:202 , HOH A:209 , HOH A:215BINDING SITE FOR RESIDUE GTP A 197
2AC2SOFTWAREMSE B:6 , ALA B:7 , GLY B:8 , GLY B:9 , LYS B:10 , GLY B:11 , THR B:12 , ARG B:13 , LYS B:19 , GLU B:82 , SER B:99 , SER B:100 , ASP B:101 , ASN B:179 , HOH B:203 , HOH B:213 , HOH B:222BINDING SITE FOR RESIDUE GTP B 197
3AC3SOFTWAREMSE C:6 , ALA C:7 , GLY C:8 , GLY C:9 , LYS C:10 , GLY C:11 , THR C:12 , ARG C:13 , LYS C:19 , SER C:99 , SER C:100 , ASP C:101 , ASN C:179 , HOH C:198 , HOH C:202BINDING SITE FOR RESIDUE GTP C 197
4AC4SOFTWAREMSE D:6 , ALA D:7 , GLY D:8 , GLY D:9 , LYS D:10 , GLY D:11 , THR D:12 , ARG D:13 , LYS D:19 , ASP D:74 , SER D:99 , SER D:100 , ASN D:179 , HOH D:215BINDING SITE FOR RESIDUE GTP D 197

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RSB)

(-) 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:177
 aligned with COBY_METJA | Q58517 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           COBY_METJA     1 MDALIMAGGKGTRMGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVIDTSGKGYIEDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPDVEALAVMIPKEKYPNPSIDFNGLVPAGINVVSPKHGYQKEEIMVIDELIFNINTKDDLKLAEMLL 191
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee----hhhhhhhhhh.ee..eehhhhhhhhhhh.....eeeee...hhhhhhhhhhhh....eeee.--------.............eeeee..ee..hhhhhhhhhhhhhhhhh...--.eeeeeee.............eeeeeeeee........eeeee.....ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rsb A   1 mDALImA----TRmGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVI--------EDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTP--EALAVmIPKEKYPNPSIDFNGLVPADINVVSPKHGYQKEEImVIDELIFNINTKDDLKLAEmLL 191
                            |    ||  - | |    20        30        40        50        60        70  |      - |      90       100       110       120    |  130  |    140       150       160       170       180       190 
                            |    ||   12 |                                                         73       82                                        125  |    |                                 169-MSE             189-MSE
                            1-MSE||     14-MSE                                                                                                           128    |                                                          
                                 6-MSE                                                                                                                        133-MSE                                                      
                                  7                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with COBY_METJA | Q58517 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           COBY_METJA     1 MDALIMAGGKGTRMGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVIDTSGKGYIEDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPDVEALAVMIPKEKYPNPSIDFNGLVPAGINVVSPKHGYQKEEIMVIDELIFNINTKDDLKLAEMLL 191
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhh..hhhh.ee..eehhhhhhhhhhhh....eeeee...hhhhhhhhhhhh....eeeee..------.....hhhhh...eeeee..ee..hhhhhhhhhhhhhhhhhhh....eeeeeee........eee..eeeeeeeee........eeeee.....ee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rsb B   1 mDALImAGGKGTRmGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVIDT------EDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPDVEALAVmIPKEKYPNPSIDFNGLVPADINVVSPKHGYQKEEImVIDELIFNINTKDDLKLAEmLL 191
                            |    |  10   |    20        30        40        50        60        70    |    - |      90       100       110       120       130  |    140       150       160       170       180       190 
                            |    |      14-MSE                                                       75     82                                                133-MSE                             169-MSE             189-MSE
                            1-MSE|                                                                                                                                                                                         
                                 6-MSE                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with COBY_METJA | Q58517 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
           COBY_METJA     1 MDALIMAGGKGTRMGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVIDTSGKGYIEDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPDVEALAVMIPKEKYPNPSIDFNGLVPAGINVVSPKHGYQKEEIMVIDELIFNINTKDDLKLAEML 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...........hhhh.ee..eehhhhhhhhhhh.....eeee....hhhhhhhhhhhh.........---------..hhhhhhh...eeeee..ee..hhhhhhhhhhhhhhhhhhh....eeeeeee.............eeeeeeeee........eeeee.....ee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rsb C   1 mDALImAGGKGTRmGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVI---------DLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPDVEALAVmIPKEKYPNPSIDFNGLVPADINVVSPKHGYQKEEImVIDELIFNINTKDDLKLAEmL 190
                            |    |  10   |    20        30        40        50        60        70  |      -  |     90       100       110       120       130  |    140       150       160       170       180       190
                            |    |      14-MSE                                                     73        83                                               133-MSE                             169-MSE             189-MSE
                            1-MSE|                                                                                                                                                                                        
                                 6-MSE                                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:180
 aligned with COBY_METJA | Q58517 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
           COBY_METJA     1 MDALIMAGGKGTRMGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVIDTSGKGYIEDLNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTPDVEALAVMIPKEKYPNPSIDFNGLVPAGINVVSPKHGYQKEEIMVIDELIFNINTKDDLKLAEML 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --NTP_transf_3-3rsbD01 D:3-184                                                                                                                                                          ------ Pfam domains (1)
           Pfam domains (2) --NTP_transf_3-3rsbD02 D:3-184                                                                                                                                                          ------ Pfam domains (2)
           Pfam domains (3) --NTP_transf_3-3rsbD03 D:3-184                                                                                                                                                          ------ Pfam domains (3)
           Pfam domains (4) --NTP_transf_3-3rsbD04 D:3-184                                                                                                                                                          ------ Pfam domains (4)
         Sec.struct. author .eeeee...........hhhh.ee..eehhhhhhhhhhhh....eeeee...hhhhhhhhhhhh....eeeee..--------..hhhhhh...eeeee..ee..hhhhhhhhhhhhhhhhhhh.--..eeeeee........eee..eeeeeeeee..........eee.....ee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rsb D   1 mDALImAGGKGTRmGGVEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPNTPKTKEYINSAYKDYKNIVVIDT--------LNECIGYFSEPFLVVSSDLINLKSKIINSIVDYFYCIKAKTP--EALAVmIPKEKYPNPSIDFNGLVPADINVVSPKHGYQKEEImVIDELIFNINTKDDLKLAEmL 190
                            |    |  10   |    20        30        40        50        60        70    |    -   |    90       100       110       120    |  130  |    140       150       160       170       180       190
                            |    |      14-MSE                                                       75       84                                      125  |    |                                 169-MSE             189-MSE
                            1-MSE|                                                                                                                       128    |                                                         
                                 6-MSE                                                                                                                        133-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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (COBY_METJA | Q58517)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0043752    adenosylcobinamide kinase activity    Catalysis of the reaction: RTP + adenosylcobinamide = adenosylcobinamide phosphate + RDP (where RTP is either ATP or GTP).
    GO:0008820    cobinamide phosphate guanylyltransferase activity    Catalysis of the reaction: adenosylcobinamide phosphate + GTP + 2 H(+) = adenosylcobinamide-GDP + diphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        COBY_METJA | Q58517: 2mzb

(-) Related Entries Specified in the PDB File

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