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(-) Description

Title :  CRYSTAL STRUCTURE OF APS KINASE FROM PENICILLIUM CHRYSOGENUM: STRUCTURE WITH APS SOAKED OUT OF ONE DIMER
 
Authors :  E. B. Lansdon, I. H. Sege, A. J. Fisher
Date :  19 Jul 02  (Deposition) - 27 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Aps Kinase, Adenylylsulfate Kinase, Transferase, Sulfate Metabolism, Nucleotide 2 Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. B. Lansdon, I. H. Segel, A. J. Fisher
Ligand-Induced Structural Changes In Adenosine 5'-Phosphosulfate Kinase From Penicillium Chrysogenum.
Biochemistry V. 41 13672 2002
PubMed-ID: 12427029  |  Reference-DOI: 10.1021/BI026556B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLYLSULFATE KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET23A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PENICILLIUM CHRYSOGENUM
    Organism Taxid: 5076
    Synonym: APS KINASE, ADENOSINE-5'PHOSPHOSULFATE KINASE, ATP ADENOSINE-5'-PHOSPHOSULFATE 3'- PHOSPHOTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ADX2Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
3SO412Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ADX1Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
3SO47Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ADX1Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
3SO45Ligand/IonSULFATE ION
Biological Unit 3 (3, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ADX1Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
3SO47Ligand/IonSULFATE ION
Biological Unit 4 (3, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ADX1Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
3SO47Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG C:80 , PHE C:105 , ILE C:106 , HOH C:1328 , HOH C:1337 , HOH C:1342BINDING SITE FOR RESIDUE SO4 C 1001
02AC2SOFTWAREARG A:66 , ARG A:80 , PHE A:105 , ILE A:106 , HOH A:1311 , HOH A:1312 , HOH A:1337 , HOH A:1367BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWARETHR B:13 , ARG B:14 , SER B:15 , THR D:13 , ARG D:14 , SER D:15BINDING SITE FOR RESIDUE SO4 B 1003
04AC4SOFTWAREHIS C:8 , ALA C:9 , SER C:10 , HOH C:1379BINDING SITE FOR RESIDUE SO4 C 1004
05AC5SOFTWAREARG A:110 , PRO A:175 , ALA A:176 , ASN A:177 , HOH A:1310 , HOH A:1376BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWAREHIS A:8 , ALA A:9 , SER A:10 , HOH B:1359BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWAREHIS B:8 , ALA B:9 , SER B:10 , ASP C:63BINDING SITE FOR RESIDUE SO4 B 1007
08AC8SOFTWAREARG C:110 , PRO C:175 , ALA C:176 , ASN C:177 , HOH C:1310 , HOH C:1363BINDING SITE FOR RESIDUE SO4 C 1008
09AC9SOFTWARETYR A:172 , GLU A:173 , ALA A:174 , HOH A:1398 , HOH A:1415 , LYS D:156BINDING SITE FOR RESIDUE SO4 A 1009
10BC1SOFTWAREASP A:63 , PHE D:7 , HIS D:8 , ALA D:9 , SER D:10BINDING SITE FOR RESIDUE SO4 D 1010
11BC2SOFTWARESER B:76 , SER C:76 , GLU C:77 , HOH C:1349BINDING SITE FOR RESIDUE SO4 C 1011
12BC3SOFTWAREGLU A:77 , HOH A:1386BINDING SITE FOR RESIDUE SO4 A 1012
13BC4SOFTWARELEU A:33 , ALA A:35 , SER A:36 , GLY A:37 , LYS A:38 , SER A:39 , THR A:40 , ARG A:148 , PRO A:150 , ASN A:184 , LEU A:187 , VAL A:189 , HOH A:1316 , HOH A:1332 , HOH A:1333 , HOH A:1351 , HOH A:1369 , ARG C:148 , ADP C:1304 , HOH C:1311 , HOH C:1364BINDING SITE FOR RESIDUE ADP A 1301
14BC5SOFTWARELEU B:33 , ALA B:35 , SER B:36 , GLY B:37 , LYS B:38 , SER B:39 , THR B:40 , ARG B:148 , PRO B:150 , LEU B:187 , HOH B:1317 , HOH B:1330 , HOH B:1341 , HOH B:1343 , HOH B:1350 , HOH B:1352 , HOH B:1382 , HOH B:1390 , HOH B:1392 , HOH B:1395 , GLU D:186BINDING SITE FOR RESIDUE ADP B 1302
15BC6SOFTWARESER B:34 , ARG B:66 , PHE B:75 , ARG B:80 , ASN B:83 , ILE B:84 , PHE B:105 , ILE B:106 , SER B:107 , PRO B:108 , LEU B:153 , LYS B:163 , GLU B:164 , THR B:166 , HOH B:1341 , HOH B:1387 , HOH B:1434BINDING SITE FOR RESIDUE ADX B 1303
16BC7SOFTWAREARG A:148 , ADP A:1301 , LEU C:33 , ALA C:35 , SER C:36 , GLY C:37 , LYS C:38 , SER C:39 , THR C:40 , ARG C:148 , ASN C:184 , LEU C:187 , HOH C:1311 , HOH C:1330 , HOH C:1338 , HOH C:1340 , HOH C:1343 , HOH C:1350 , HOH C:1364 , HOH C:1413BINDING SITE FOR RESIDUE ADP C 1304
17BC8SOFTWAREGLU B:186 , LEU D:33 , ALA D:35 , SER D:36 , GLY D:37 , LYS D:38 , SER D:39 , THR D:40 , ARG D:148 , PRO D:150 , ASN D:184 , LEU D:187 , HOH D:1327 , HOH D:1335 , HOH D:1336 , HOH D:1337 , HOH D:1351 , HOH D:1353 , HOH D:1359 , HOH D:1381 , HOH D:1402BINDING SITE FOR RESIDUE ADP D 1305
18BC9SOFTWARESER D:34 , ARG D:66 , PHE D:75 , ARG D:80 , ASN D:83 , ILE D:84 , PHE D:105 , ILE D:106 , SER D:107 , PRO D:108 , LEU D:153 , ILE D:162 , LYS D:163 , GLU D:164 , PHE D:165 , THR D:166 , HOH D:1337 , HOH D:1346 , HOH D:1358BINDING SITE FOR RESIDUE ADX D 1306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M7H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M7H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M7H)

(-) Exons   (0, 0)

(no "Exon" information available for 1M7H)

(-) 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:203
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:203
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
           KAPS_PENCH     7 FHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
               SCOP domains d1m7ha_ A: Adenosine-5'phosphosulfate kinase (APS kinase)                                                                                                                                                   SCOP domains
               CATH domains 1m7hA00 A:7-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh.....eeeehhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..........eeeeeee.hhhhhhhhh..hhhhhhh.....................eeee....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m7h A   7 FHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:206
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
           KAPS_PENCH     6 TFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKKE 211
               SCOP domains d1m7hb_ B: Adenosine-5'phosphosulfate kinase (APS kinase)                                                                                                                                                      SCOP domains
               CATH domains 1m7hB00 B:6-211 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh....eeeehhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh------....eeeeeee.hhhhhhhhh..hhhhhhhh....................eeee....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m7h B   6 TFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEV------TGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKKE 211
                                    15        25        35        45        55        65        75        85        95       105       115      |  -   |   135       145       155       165       175       185       195       205      
                                                                                                                                              122    129                                                                                  


Chain C from PDB  Type:PROTEIN  Length:204
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:204
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
           KAPS_PENCH     6 TFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
               SCOP domains d1m7hc_ C: Adenosine-5'phosphosulfate kinase (APS kinase)                                                                                                                                                    SCOP domains
               CATH domains 1m7hC00 C:6-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh.....eeeeehhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..........eeeeeee.hhhhhhhhh..hhhhhhhh....................eeee....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m7h C   6 TFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    


Chain D from PDB  Type:PROTEIN  Length:198
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:204
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
           KAPS_PENCH     6 TFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
               SCOP domains d1m7hd_ D: Adenosine-5'phosphosulfate kinase (APS kinase)                                                                                                                                                    SCOP domains
               CATH domains 1m7hD00 D:6-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
           Pfam domains (1) ------------------APS_kinase-1m7hD01 D:24-189                                                                                                                                           -------------------- Pfam domains (1)
           Pfam domains (2) ------------------APS_kinase-1m7hD02 D:24-189                                                                                                                                           -------------------- Pfam domains (2)
           Pfam domains (3) ------------------APS_kinase-1m7hD03 D:24-189                                                                                                                                           -------------------- Pfam domains (3)
           Pfam domains (4) ------------------APS_kinase-1m7hD04 D:24-189                                                                                                                                           -------------------- Pfam domains (4)
         Sec.struct. author .......hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh.....eeeehhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh------....eeeeeee.hhhhhhhhh..hhhhhhhh....................eeee....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m7h D   6 TFHASALTRSERTELRNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEV------TGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
                                    15        25        35        45        55        65        75        85        95       105       115      |  -   |   135       145       155       165       175       185       195       205    
                                                                                                                                              122    129
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  1m7h
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  KAPS_PENCH | Q12657
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  KAPS_PENCH | Q12657
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        KAPS_PENCH | Q12657: 1d6j 1m7g 3cr7

(-) Related Entries Specified in the PDB File

1d6j APO CRYSTAL STRUCTURE
1m7g CRYSTAL STRUCTURE OF APS KINASE FROM PENICILLIUM CHRYSOGENUM: TERNARY STRUCTURE WITH ADP AND APS