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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF ATP:CORRINOID ADENOSYLTRANSFERASE FROM SALMONELLA TYPHIMURIUM. COBALAMIN/ATP TERNARY COMPLEX
 
Authors :  I. Rayment, J. C. Escalante-Semerena, C. B. Bauer
Date :  03 Nov 00  (Deposition) - 20 Dec 00  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  P-Loop Protein, Cobalamin Biosynthesis, Reca Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. B. Bauer, M. V. Fonseca, H. M. Holden, J. B. Thoden, T. B. Thompson, J. C. Escalante-Semerena, I. Rayment
Three-Dimensional Structure Of Atp:Corrinoid Adenosyltransferase From Salmonella Typhimurium In Its Free State, Complexed With Mgatp, Or Complexed With Hydroxycobalamin And Mgatp.
Biochemistry V. 40 361 2001
PubMed-ID: 11148030  |  Reference-DOI: 10.1021/BI002145O

(-) Compounds

Molecule 1 - COB(I)ALAMIN ADENOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.17
    Engineered: YES
    Expression System: SALMONELLA TYPHIMURIUM
    Expression System Taxid: 602
    Gene: COBA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: CORRINOID ADENOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2B121Ligand/IonCOBALAMIN
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:42 , GLU A:128 , ATP A:999 , HOH A:1331 , HOH A:1332BINDING SITE FOR RESIDUE MG A 998
2AC2SOFTWARETHR B:242 , GLU B:328 , ATP B:1000 , HOH B:1380 , HOH B:1381BINDING SITE FOR RESIDUE MG B 1001
3AC3SOFTWARELYS A:66 , TRP A:93 , TYR A:131 , ARG A:161 , ATP A:999 , HOH A:1239 , ARG B:216 , PRO B:279 , HIS B:280 , GLN B:296BINDING SITE FOR RESIDUE B12 A 800
4AC4SOFTWAREASN A:37 , GLY A:38 , LYS A:39 , GLY A:40 , LYS A:41 , THR A:42 , THR A:43 , GLU A:128 , ARG A:161 , HIS A:182 , ASP A:195 , B12 A:800 , MG A:998 , HOH A:1247 , HOH A:1331 , HOH A:1332 , HOH A:1421 , ARG B:251BINDING SITE FOR RESIDUE ATP A 999
5AC5SOFTWAREARG A:51 , ASN B:237 , GLY B:238 , LYS B:239 , GLY B:240 , LYS B:241 , THR B:242 , THR B:243 , GLU B:328 , TYR B:331 , HIS B:382 , ASP B:395 , MG B:1001 , HOH B:1214 , HOH B:1367 , HOH B:1380 , HOH B:1381BINDING SITE FOR RESIDUE ATP B 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G64)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G64)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G64)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G64)

(-) Exons   (0, 0)

(no "Exon" information available for 1G64)

(-) 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:169
 aligned with BTUR_SALTY | P31570 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:169
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187         
           BTUR_SALTY    28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLADTVSELRPVKHAFDAGVKAQMGIDY 196
               SCOP domains d1g64a_ A: ATP:corrinoid adenosyltransferase CobA                                                                                                                         SCOP domains
               CATH domains 1g64A00 A:28-196 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhhh....eeeee.......hhhhhhhh....eee...........hhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhh...hhhhhhhhhhh.....eeeee....hhhhhhhh.eeeeeeeeehhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g64 A  28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLADTVSELRPVKHAFDAGVKAQMGIDY 196
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187         


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with BTUR_SALTY | P31570 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:190
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196
           BTUR_SALTY     7 QQRQQKVKDRVDARVAQAQEERGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLADTVSELRPVKHAFDAGVKAQMGIDY 196
               SCOP domains d1g64b_ B: ATP:corrinoid adenosyltransferase CobA                                                                                                                                              SCOP domains
               CATH domains 1g64B00 B:207-396 P-loop containing nucleotide triphosphate hydrolases                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhh...hhhhhhhhhhhh....eeeee....hhhhhhhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g64 B 207 QQRQQKVKDRVDARVAQAQEERGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLADTVSELRPVKHAFDAGVKAQMGIDY 396
                                   216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G64)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BTUR_SALTY | P31570)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008817    cob(I)yrinic acid a,c-diamide adenosyltransferase activity    Catalysis of the reaction: ATP + cob(I)alamin + H2O = phosphate + diphosphate + adenosylcobalamin.
    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:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        BTUR_SALTY | P31570: 1g5r 1g5t 4hut

(-) Related Entries Specified in the PDB File

1g5r APO COBA
1g5t COBA ATP COMPLEX