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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF COBT IN COMPLEX WITH 5-METHOXYBENZIMIDAZOLE
 
Authors :  C. G. Cheong, J. Escalante-Semerena, I. Rayment
Date :  28 Jun 01  (Deposition) - 18 Oct 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cobt, Cobalamin Biosynthesis, Lower Ligand, Cobamides, Nn:Dbi Prt, N1-Alpha-Phosphoribosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Cheong, J. C. Escalante-Semerena, I. Rayment
Structural Investigation Of The Biosynthesis Of Alternative Lower Ligands For Cobamides By Nicotinate Mononucleotide: 5, 6-Dimethylbenzimidazole Phosphoribosyltransferase From Salmonella Enterica.
J. Biol. Chem. V. 276 37612 2001
PubMed-ID: 11441022  |  Reference-DOI: 10.1074/JBC.M105390200

(-) Compounds

Molecule 1 - NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.21
    Engineered: YES
    Expression System: SALMONELLA ENTERICA
    Expression System Taxid: 28901
    Organism Scientific: SALMONELLA ENTERICA
    Organism Taxid: 28901
    Phosphoribosyltransferase, Nn: DBI PRT
    Synonym: NICOTINATE-NUCLEOTIDE--DIMETHYLBENZIMIDAZOLE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
15OB1Ligand/Ion5-METHOXYBENZIMIDAZOLE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
15OB2Ligand/Ion5-METHOXYBENZIMIDAZOLE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:264 , PHE A:265 , LEU A:266 , SER A:291 , ARG A:314 , LEU A:315 , GLY A:316 , HOH A:1002BINDING SITE FOR RESIDUE PO4 A 991
2AC2SOFTWAREALA A:78 , ALA A:178 , ASN A:179 , THR A:180 , GLY A:202 , ALA A:203 , HOH A:1027 , HOH A:1028 , HOH A:1064BINDING SITE FOR RESIDUE PO4 A 992
3AC3SOFTWAREPRO A:32 , SER A:80 , GLN A:88 , LEU A:315 , GLU A:317 , LEU A:348BINDING SITE FOR RESIDUE 5OB A 990

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:160 -A:256

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JHP)

(-) 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 COBT_SALTY | Q05603 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:346
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343      
           COBT_SALTY     4 LHALLRDIPAPDAEAMARAQQHIDGLLKPPGSLGRLETLAVQLAGMPGLNGTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLAAQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLLEVSRYTCDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGANLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGAARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHLSMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLP 349
               SCOP domains d1jhpa_ A: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1jhpA01 A:4-57,A:330-349                              1jhpA02 A:58-329  [code=3.40.50.10210, no name defined]                                                                                                                                                                                                                         1jhpA01              CATH domains
               Pfam domains ---DBI_PRT-1jhpA01 A:7-346                                                                                                                                                                                                                                                                                                                             --- Pfam domains
         Sec.struct. author hhhhhhh....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh......eeeeeeeee..hhhhhh......hhhhhhhhhhh...hhhhhhhhhhh..................ee.......................................eeeeeeeee...hhhhhhhhhhhhhh.hhhhhh......hhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jhp A   4 LHALLRDIPAPDAEAMARTQQHIDGLLKPPGSLGRLETLAVQLAGMPGLNGTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLAAQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLLEVSRYTCDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGANLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGAARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHLSMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLP 349
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   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, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (COBT_SALTY | Q05603)
molecular function
    GO:0015420    cobalamin-transporting ATPase activity    Catalysis of the reaction: ATP + H2O + cob(III)alamin(out) = ADP + phosphate + cob(III)alamin(in). Cobalamin is also known as vitamin B12.
    GO:0008939    nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity    Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0015889    cobalamin transport    The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0009163    nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0035461    vitamin transmembrane transport    The process in which a vitamin is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.

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  1jhp
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  COBT_SALTY | Q05603
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  2.4.2.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        COBT_SALTY | Q05603: 1d0s 1d0v 1jh8 1jha 1jhm 1jho 1jhq 1jhr 1jhu 1jhv 1jhx 1jhy 1l4b 1l4e 1l4f 1l4g 1l4h 1l4k 1l4l 1l4m 1l4n 1l5f 1l5k 1l5l 1l5m 1l5n 1l5o 4kqf 4kqg 4kqh 4kqi 4kqj 4kqk

(-) Related Entries Specified in the PDB File

1d0s COBT COMPLEXED WITH DIMETHYLBENZIMIDAZOLE
1d0v
1jh8
1jha
1jhm
1jho
1jhq
1jhr
1jhu
1jhv
1jhx
1jhy