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(-) Description

Title :  ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE (COBU) FROM SALMONELLA TYPHIMURIUM
 
Authors :  T. B. Thompson, M. G. Thomas, J. C. Escalante-Semerena, I. Rayment
Date :  12 Mar 98  (Deposition) - 02 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cobalamin Biosynthesis, Adenosylcobinamide, Kinase, Atpase, Guanylyltransferase, Salmonella Typhimurium, Transferase, Coenzyme B12 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. B. Thompson, M. G. Thomas, J. C. Escalante-Semerena, I. Rayment
Three-Dimensional Structure Of Adenosylcobinamide Kinase/Adenosylcobinamide Phosphate Guanylyltransferase From Salmonella Typhimurium Determined To 2. 3 A Resolution, .
Biochemistry V. 37 7686 1998
PubMed-ID: 9601028  |  Reference-DOI: 10.1021/BI973178F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: LT2
    Expression System Taxid: 562
    Expression System Vector: T7-7
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:9 , SER A:10 , GLY A:11 , LYS A:12 , SER A:13 , HOH A:692 , GLN C:559BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWAREHOH A:783 , ARG B:209 , SER B:210 , GLY B:211 , LYS B:212 , SER B:213BINDING SITE FOR RESIDUE SO4 B 802
3AC3SOFTWAREHOH B:648 , ARG C:409 , SER C:410 , GLY C:411 , LYS C:412 , SER C:413BINDING SITE FOR RESIDUE SO4 C 803

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:80 -Cys A:81
2Glu B:280 -Cys B:281
3Glu C:480 -Cys C:481

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CBU)

(-) 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:180
 aligned with COBU_SALTY | Q05599 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           COBU_SALTY     2 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 181
               SCOP domains d1cbua_ A: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU                                                                                           SCOP domains
               CATH domains 1cbuA00 A:1-180 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhh....eeeeee..hhhhhhhhhhhhhh......eeeeee....hhh..........eeeee.hhhhhhhhhhhhh....hhh..hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhh..eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cbu A   1 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with COBU_SALTY | Q05599 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           COBU_SALTY     2 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 181
               SCOP domains d1cbub_ B: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU                                                                                           SCOP domains
               CATH domains 1cbuB00 B:201-380 P-loop containing nucleotide triphosphate hydrolases                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhh...eeeeee....hhh..........eeeee.hhhhhhhhhhhhh....hhh..hhhhhhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhhhhhhhhhhh..eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cbu B 201 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 380
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380


Chain C from PDB  Type:PROTEIN  Length:179
 aligned with COBU_SALTY | Q05599 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           COBU_SALTY     2 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 181
               SCOP domains d1cbuc_ C: Adenosylcobinamide kinase/adenosylc obinamide phosphate guanylyltransferase CobU                                                                                          SCOP domains
               CATH domains 1cbuC00 C:401-580 P-loop containing nucleotide  triphosphate hydrolases                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhh....eeeeee..hhhhhhhhhh....-.....eeeeee....hhh..........eeeee.hhhhhhhhhhhh.....hhh..hhhhhhhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhhhhhhhhhhh..eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cbu C 401 MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHH-DGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK 580
                                   410       420       430       440     | 450       460       470       480       490       500       510       520       530       540       550       560       570       580
                                                                       446 |                                                                                                                                    
                                                                         448
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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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CBU)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (COBU_SALTY | Q05599)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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.
    GO:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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 Related Entries

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        COBU_SALTY | Q05599: 1c9k

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