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(-) Description

Title :  STRUCTURE OF HUMAN ATP:COBALAMIN ADENOSYLTRANSFERASE BOUND TO ATP.
 
Authors :  H. L. Schubert, C. P. Hill
Date :  15 Sep 06  (Deposition) - 06 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Atp, Cobalamin, Adenosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Schubert, C. P. Hill
Structure Of Atp-Bound Human Atp:Cobalamin Adenosyltransferase.
Biochemistry V. 45 15188 2006
PubMed-ID: 17176040  |  Reference-DOI: 10.1021/BI061396F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COB(I)YRINIC ACID A,C-DIAMIDE ADENOSYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.5.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MMAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COBI, ALAMIN ADENOSYLTRANSFERASE, METHYLMALONIC ACIDURIA TYPE B PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:108 , THR A:109 , PHE A:110 , TYR A:226BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREHIS C:108 , THR C:109 , PHE C:110 , TYR C:226BINDING SITE FOR RESIDUE SO4 C 402
03AC3SOFTWAREHIS B:108 , THR B:109 , PHE B:110 , TYR B:226 , HOH B:627BINDING SITE FOR RESIDUE SO4 B 403
04AC4SOFTWAREARG A:195 , ARG B:195 , ARG C:195BINDING SITE FOR RESIDUE CL A 601
05AC5SOFTWAREASN A:214 , ATP A:607 , HOH A:633 , HOH A:634BINDING SITE FOR RESIDUE MG A 603
06AC6SOFTWAREATP B:606 , ASN C:214 , HOH C:652 , HOH C:672BINDING SITE FOR RESIDUE MG C 604
07AC7SOFTWAREILE B:58 , ATP B:606 , HOH B:659 , HOH B:669 , HOH B:670 , HOH C:665BINDING SITE FOR RESIDUE MG B 605
08AC8SOFTWAREATP A:607 , HOH A:608 , HOH A:631 , HOH A:632 , HOH A:639BINDING SITE FOR RESIDUE MG A 606
09AC9SOFTWAREARG A:190 , GLU A:193 , ARG A:194 , ASN A:214 , MG A:603 , MG A:606 , HOH A:608 , HOH A:631 , HOH A:632 , HOH A:633 , HOH A:634 , LYS C:61 , THR C:62 , GLY C:63 , PHE C:67 , SER C:68 , SER C:69 , LYS C:78 , PHE C:83 , HOH C:612 , HOH C:673BINDING SITE FOR RESIDUE ATP A 607
10BC1SOFTWARETHR B:60 , LYS B:61 , THR B:62 , GLY B:63 , SER B:68 , SER B:69 , LYS B:78 , PHE B:83 , SER B:162 , MG B:605 , HOH B:630 , HOH B:634 , HOH B:659 , HOH B:669 , HOH B:670 , ARG C:190 , GLU C:193 , ARG C:194 , ASN C:214 , MG C:604 , HOH C:652 , HOH C:672BINDING SITE FOR RESIDUE ATP B 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IDX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IDX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 17)

Asymmetric/Biological Unit (6, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023471I96TMMAB_HUMANDisease (MMAB)864309509A/B/CI96T
2UniProtVAR_017204A135TMMAB_HUMANDisease (MMAB)35648932B/CA135T
3UniProtVAR_017205R186WMMAB_HUMANPolymorphism28941784A/B/CR186W
4UniProtVAR_017206R191WMMAB_HUMANDisease (MMAB)376128990A/B/CR191W
5UniProtVAR_017207E193KMMAB_HUMANDisease (MMAB)749758687A/B/CE193K
6UniProtVAR_017208M239KMMAB_HUMANPolymorphism9593A/B/CM239K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IDX)

(-) Exons   (0, 0)

(no "Exon" information available for 2IDX)

(-) 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:148
 aligned with MMAB_HUMAN | Q96EY8 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:162
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  
           MMAB_HUMAN    79 DDQVFEAVGTTDELSSAIGFALELVTEKGHTFAEELQKIQCTLQDVGSALATPCSSAREAHLKYTTFKAGPILELEQWIDKYTSQLPPLTAFILPSGGKISSALHFCRAVCRRAERRVVPLVQMGETDANVAKFLNRLSDYLFTLARYAAMKEGNQEKIYMK 240
               SCOP domains d2idxa_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains 2idxA00 A:79-240  [code=1.20.1200.10, no name defin              ed]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh--------------...hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -----------------T-----------------------------------------------------------------------------------------W----W-K---------------------------------------------K- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2idx A  79 DDQVFEAVGTTDELSSAIGFALELVTEKGHTFAEELQKIQCTLQDVGSALA--------------TFKAGPILELEQWIDKYTSQLPPLTAFILPSGGKISSALHFCRAVCRRAERRVVPLVQMGETDANVAKFLNRLSDYLFTLARYAAMKEGNQEKIYMK 240
                                    88        98       108       118       128|        -     | 148       158       168       178       188       198       208       218       228       238  
                                                                            129            144                                                                                                


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with MMAB_HUMAN | Q96EY8 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:184
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    
           MMAB_HUMAN    57 KIYTKTGDKGFSSTFTGERRPKDDQVFEAVGTTDELSSAIGFALELVTEKGHTFAEELQKIQCTLQDVGSALATPCSSAREAHLKYTTFKAGPILELEQWIDKYTSQLPPLTAFILPSGGKISSALHFCRAVCRRAERRVVPLVQMGETDANVAKFLNRLSDYLFTLARYAAMKEGNQEKIYMK 240
               SCOP domains d2idxb_ B: automated matches                                                                                                                                                             SCOP domains
               CATH domains ----------2idxB01 B:67-240  [code=1.20.1200.10, no name defined]                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....eee..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......------.....hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------T--------------------------------------T--------------------------------------------------W----W-K---------------------------------------------K- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2idx B  57 KIYTKTGDKGFSSTFTGERRPKDDQVFEAVGTTDELSSAIGFALELVTEKGHTFAEELQKIQCTLQDVGSALATPCSSA------YTTFKAGPILELEQWIDKYTSQLPPLTAFILPSGGKISSALHFCRAVCRRAERRVVPLVQMGETDANVAKFLNRLSDYLFTLARYAAMKEGNQEKIYMK 240
                                    66        76        86        96       106       116       126        |-     | 146       156       166       176       186       196       206       216       226       236    
                                                                                                        135    142                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:180
 aligned with MMAB_HUMAN | Q96EY8 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:183
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237   
           MMAB_HUMAN    58 IYTKTGDKGFSSTFTGERRPKDDQVFEAVGTTDELSSAIGFALELVTEKGHTFAEELQKIQCTLQDVGSALATPCSSAREAHLKYTTFKAGPILELEQWIDKYTSQLPPLTAFILPSGGKISSALHFCRAVCRRAERRVVPLVQMGETDANVAKFLNRLSDYLFTLARYAAMKEGNQEKIYMK 240
               SCOP domains d2idxc_ C: automated matches                                                                                                                                                            SCOP domains
               CATH domains ---------2idxC01 C:67-240  [code=1.20.1200.10,    no name defined]                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.....eee..hhhhhhhhhhhhhhhhhhhhhh...---hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------T--------------------------------------T--------------------------------------------------W----W-K---------------------------------------------K- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2idx C  58 IYTKTGDKGFSSTFTGERRPKDDQVFEAVGTTDELSSAIGFALELVT---HTFAEELQKIQCTLQDVGSALATPCSSAREAHLKYTTFKAGPILELEQWIDKYTSQLPPLTAFILPSGGKISSALHFCRAVCRRAERRVVPLVQMGETDANVAKFLNRLSDYLFTLARYAAMKEGNQEKIYMK 240
                                    67        77        87        97      |  -|      117       127       137       147       157       167       177       187       197       207       217       227       237   
                                                                        104 108
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IDX)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (MMAB_HUMAN | Q96EY8)
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:0009235    cobalamin metabolic process    The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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