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(-) Description

Title :  CRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FROM PENICILLIUM CHRYSOGENUM
 
Authors :  I. J. Macrae, I. H. Segel, A. J. Fisher
Date :  13 Oct 99  (Deposition) - 23 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aps Kinase, Adenylylsulfate Kinase, Sulfate, Nucleotide Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. J. Macrae, I. H. Segel, A. J. Fisher
Crystal Structure Of Adenosine 5'-Phosphosulfate Kinase From Penicillium Chrysogenum.
Biochemistry V. 39 1613 2000
PubMed-ID: 10677210  |  Reference-DOI: 10.1021/BI9924157
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOSINE-5'PHOSPHOSULFATE KINASE
    Chains: A, B
    EC Number: 2.7.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Taxid: 562
    Organism Scientific: PENICILLIUM CHRYSOGENUM
    Organism Taxid: 5076
    Synonym: APS KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:62 , ARG A:66 , SER A:104 , PHE A:105 , ILE A:106 , HOH A:282 , HOH A:301 , HOH A:302BINDING SITE FOR RESIDUE TLA A 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D6J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D6J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D6J)

(-) Exons   (0, 0)

(no "Exon" information available for 1D6J)

(-) 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:177
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
           KAPS_PENCH     8 HASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKK 210
               SCOP domains d1d6ja_ A: Adenosine-5'phosphosulfate kinase (APS kinase)                                                                                                                                                   SCOP domains
               CATH domains 1d6jA00 A:8-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh..........eeeeeee....--------------------------..........eeee....hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d6j A   8 HASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVE--------------------------APYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKK 210
                                    17        27        37        47        57        67        77        87        97       107       117       127       137     |   -         -         -  |    177       187       197       207   
                                                                                                                                                                 143                        170                                        


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
           KAPS_PENCH     8 HASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKK 210
               SCOP domains d1d6jb_ B: Adenosine-5'phosphosulfate kinase (APS kinase)                                                                                                                                                   SCOP domains
               CATH domains 1d6jB00 B:8-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh.....eee..hhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh..........eeeeeee.hhhhhh..---------------------..........eeee....hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d6j B   8 HASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQR---------------------APYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKK 210
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147|        -         -  |    177       187       197       207   
                                                                                                                                                                      148                   170
   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 1D6J)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KAPS_PENCH | Q12657)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0098617    adenylylselenate kinase activity    Catalysis of the reaction: ATP + Adenylylselenate => ADP + 3'-Phosphoadenylylselenate.
    GO:0004020    adenylylsulfate kinase activity    Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
    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:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019344    cysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0070814    hydrogen sulfide biosynthetic process    The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    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.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAPS_PENCH | Q12657: 1m7g 1m7h 3cr7

(-) Related Entries Specified in the PDB File

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