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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST PAPS REDUCTASE WITH PAP, A PRODUCT COMPLEX
 
Authors :  Z. Yu, A. J. Fisher
Date :  31 Jan 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sulfate Reduction, Paps Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yu, D. Lemongello, I. H. Segel, A. J. Fisher
Crystal Structure Of Saccharomyces Cerevisiae 3'-Phosphoadenosine-5'-Phosphosulfate Reductase Complexed With Adenosine 3', 5'-Bisphosphate.
Biochemistry V. 47 12777 2008
PubMed-ID: 18991405  |  Reference-DOI: 10.1021/BI801118F

(-) Compounds

Molecule 1 - PHOSPHOADENOSINE PHOSPHOSULFATE REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.8.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB2
    Expression System Strain: BL21 DE3 CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MET16
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: CRY1
    Synonym: PAPS REDUCTASE, THIOREDOXIN DEPENDENT, PADOPS REDUCTASE, 3'- PHOSPHOADENYLYLSULFATE REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1A3P4Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:47 , THR A:48 , ALA A:49 , PHE A:50 , GLY A:51 , GLY A:54 , ILE A:76 , LYS A:139 , THR A:157 , GLY A:158 , ARG A:167 , ARG A:236 , ILE A:247 , HIS A:248 , HOH A:1008 , HOH A:1018 , HOH A:1024 , HOH A:1025 , HOH A:1034 , HOH A:1039 , HOH A:1071BINDING SITE FOR RESIDUE A3P A 999
2AC2SOFTWARETHR B:47 , THR B:48 , ALA B:49 , PHE B:50 , GLY B:51 , GLY B:54 , ILE B:76 , THR B:157 , GLY B:158 , ARG B:159 , ARG B:167 , ARG B:233 , ARG B:236 , HIS B:248 , HOH B:1010 , HOH B:1028 , HOH B:1031BINDING SITE FOR RESIDUE A3P B 999
3AC3SOFTWARETHR C:47 , THR C:48 , ALA C:49 , PHE C:50 , GLY C:51 , GLY C:54 , ILE C:76 , THR C:157 , GLY C:158 , ARG C:167 , ARG C:236 , ILE C:247 , HIS C:248 , HOH C:1004 , HOH C:1034 , HOH C:1039 , HOH C:1050 , HOH C:1092 , HOH C:1097 , HOH C:1127 , HOH C:1139BINDING SITE FOR RESIDUE A3P C 999
4AC4SOFTWARETHR D:47 , THR D:48 , ALA D:49 , PHE D:50 , GLY D:51 , GLY D:54 , LEU D:74 , ILE D:76 , THR D:157 , GLY D:158 , ARG D:167 , ARG D:236 , HIS D:248 , HOH D:1000 , HOH D:1010BINDING SITE FOR RESIDUE A3P D 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OQ2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly D:123 -Asp D:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OQ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OQ2)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR167C1YPR167C.1XVI:877628-876843786MET16_YEAST1-2612614A:1-256 (gaps)
B:1-259 (gaps)
C:1-257
D:1-253 (gaps)		256
259
257
253

(-) 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:251
 aligned with MET16_YEAST | P18408 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
          MET16_YEAST     1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRWKGKAKTECGIHEASRFAQF 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh.eeehhhhhhhhhhhh...hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh..eeee....eeee......hhhhhhhhhhhhh...hhhhhhh.....hhhhh..............-----.......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-256 (gaps) UniProt: 1-261 [INCOMPLETE]                                                                                                                                                                                                        Transcript 1
                 2oq2 A   1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRW-----TECGIHEASRFAQF 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      |  -  |    250      
                                                                                                                                                                                                                                                                      237   243             


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with MET16_YEAST | P18408 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
          MET16_YEAST     1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRWKGKAKTECGIHEASRFAQFLKQ 259
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh.eeehhhhhhhhhhhh...hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh..eeee....eeee......hhhhhhhhhhhh....hhhhhhh........................-------....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-259 (gaps) UniProt: 1-261 [INCOMPLETE]                                                                                                                                                                                                           Transcript 1
                 2oq2 B   1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRW-------CGIHEASRFAQFLKQ 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      |  -    |  250         
                                                                                                                                                                                                                                                                      237     245              


Chain C from PDB  Type:PROTEIN  Length:257
 aligned with MET16_YEAST | P18408 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
          MET16_YEAST     1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRWKGKAKTECGIHEASRFAQFL 257
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh.eeehhhhhhhhhhhh...hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhh..eeee....eeee......hhhhhhhhhhhh....hhhhhhh.....hhhhh..........................hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-257 UniProt: 1-261 [INCOMPLETE]                                                                                                                                                                                                                Transcript 1
                 2oq2 C   1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRWKGKAKTECGIHEASRFAQFL 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       


Chain D from PDB  Type:PROTEIN  Length:246
 aligned with MET16_YEAST | P18408 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          MET16_YEAST     1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGRWKGKAKTECGIHEASRF 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------PAPS_reduct-2oq2D01 D:43-225                                                                                                                                                           ---------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------PAPS_reduct-2oq2D02 D:43-225                                                                                                                                                           ---------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------PAPS_reduct-2oq2D03 D:43-225                                                                                                                                                           ---------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------PAPS_reduct-2oq2D04 D:43-225                                                                                                                                                           ---------------------------- Pfam domains (4)
         Sec.struct. author ..eee.hhh.eeehhhhhhhhhhhh...hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh..eeee....eeee......hhhhhhhhhhhh....hhhhhhh.......................-------.....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-253 (gaps) UniProt: 1-261 [INCOMPLETE]                                                                                                                                                                                                     Transcript 1
                 2oq2 D   1 MKTYHLNNDIIVTQEQLDHWNEQLIKLETPQEIIAWSIVTFPHLFQTTAFGLTGLVTIDMLSKLSEKYYMPELLFIDTLHHFPQTLTLKNEIEKKYYQPKNQTIHVYKPDGCESEADFASKYGDFLWEKDDDKYDYLAKVEPAHRAYKELHISAVFTGRRKSQGSARSQLSIIEIDELNGILKINPLINWTFEQVKQYIDANNVPYNELLDLGYRSIGDYHSTQPVKEGEDERAGR-------ECGIHEASRF 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     |   -   |   250   
                                                                                                                                                                                                                                                                     236     244
   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  (0, 0)

(no "SCOP Domain" information available for 2OQ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OQ2)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MET16_YEAST | P18408)
molecular function
    GO:0098624    3'-Phosphoadenylylselenate reductase activity    Catalysis of the reaction: 3'-Phosphoadenylylselenate + NADPH => Adenosine 3',5'-bisphosphate + Selenite + NADP+ + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004604    phosphoadenylyl-sulfate reductase (thioredoxin) activity    Catalysis of the reaction: adenosine 3',5'-diphosphate + H(+) + sulfite + thioredoxin disulfide = 3'-phospho-5'-adenylyl sulfate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin; 3'-phosphoadenosine 5'-phosphosulfate is also known as PAPS.
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:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
    GO:0070814    hydrogen sulfide biosynthetic process    The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0001887    selenium compound metabolic process    The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine.
    GO:0019379    sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin)    The pathway by which inorganic sulfate is processed and incorporated into sulfated compounds, where the phosphoadenylyl sulfate reduction step is catalyzed by the enzyme phosphoadenylyl-sulfate reductase (thioredoxin) (EC:1.8.4.8).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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