PAPSS1 (Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1) — review notes

UniProt: O43252 (PAPS1_HUMAN). Gene: PAPSS1 (synonyms ATPSK1, PAPSS). Human, NCBITaxon:9606.

Summary of function

PAPSS1 is a cytosolic and nuclear bifunctional enzyme that synthesizes PAPS (3'-phosphoadenosine
5'-phosphosulfate), the universal activated sulfate donor for all cytosolic and Golgi sulfotransferases.
Two catalytic domains act sequentially in the sulfate-activation pathway:

1. ATP sulfurylase / sulfate adenylyltransferase (ATP) domain (C-terminal, residues ~234–624):
   sulfate + ATP + H(+) -> adenosine 5'-phosphosulfate (APS) + diphosphate (EC 2.7.7.4).
2. APS kinase / adenylyl-sulfate kinase domain (N-terminal, residues 1–225):
   APS + ATP -> 3'-phosphoadenylyl sulfate (PAPS) + ADP + H(+) (EC 2.7.1.25).

[file:human/PAPSS1/PAPSS1-uniprot.txt "Bifunctional enzyme with both ATP sulfurylase and APS kinase
activity, which mediates two steps in the sulfate activation pathway."]
[file:human/PAPSS1/PAPSS1-uniprot.txt "In mammals, PAPS is the sole source of sulfate; APS appears to be only an intermediate in the sulfate-activation pathway"]

Domain assignment and boundaries from UniProt FT REGION:
- REGION 1..225 "Adenylyl-sulfate kinase"
- REGION 234..624 "Sulfate adenylyltransferase"
[file:human/PAPSS1/PAPSS1-uniprot.txt]

Note the domain order in the primary sequence is unusual for the animal fusion: the APS kinase
domain is N-terminal and the ATP sulfurylase domain is C-terminal
PMID:9648242
PMID:9668121

Catalytic activity (verbatim, UniProt)

• [file:human/PAPSS1/PAPSS1-uniprot.txt "Reaction=sulfate + ATP + H(+) = adenosine 5'-phosphosulfate +"] (EC 2.7.7.4, RHEA:18133)
• [file:human/PAPSS1/PAPSS1-uniprot.txt "Reaction=adenosine 5'-phosphosulfate + ATP = 3'-phosphoadenylyl sulfate"] (EC 2.7.1.25, RHEA:24152)

Pathway

Sulfur metabolism; sulfate assimilation. UniProt PATHWAY + UniPathway UPA00097.
[file:human/PAPSS1/PAPSS1-uniprot.txt "Sulfur metabolism; sulfate assimilation."]

PAPS is the sole physiological sulfonate donor; it feeds sulfation of glycosaminoglycans/proteoglycans,
sulfomucins, steroids, tyrosine, neurotransmitters, hormones, drugs and xenobiotics.
PMID:9576487

Biochemical / structural evidence

• Both activities and PAPS synthesis demonstrated on the recombinant human enzyme
  PMID:9576487
• Recombinant full-length and each isolated domain shown to carry their respective activities
  PMID:9648242
• Full-length enzyme is a homodimer and is catalytically active (25 nmol PAPS/min/mg)
  PMID:14747722
  UniProt SUBUNIT: [file:human/PAPSS1/PAPSS1-uniprot.txt "Homodimer."]
• APS kinase domain crystal structures (Michaelis complex with ADP-Mg + PAPS; APS-bound)
  PMID:17276460
• APS kinase is uncompetitively substrate-inhibited by APS; N-terminal residues R37/R40 mediate this
  PMID:17540769
  UniProt DOMAIN: [file:human/PAPSS1/PAPSS1-uniprot.txt "The N-terminal first 50 residues are required for inhibition by"]
• ATP-sulfurylase HXGH motif (His425/His428) is essential; H425A and H428A abolish activity
  (UniProt MUTAGEN, PMID:9915785).

Subcellular localization

• Both cytosol and nucleus, experimentally (dynamic shuttling)
  [PMID:22242175 title "Human PAPS synthase isoforms are dynamically regulated enzymes with access to nucleus and cytoplasm."]
• PAPSS1 accumulates in the nucleus; nuclear targeting mediated by the APS kinase domain and an
  N-terminal 21-aa sequence
  PMID:10657990
  PMID:10657990

Tissue specificity

Wide distribution; testis, pancreas, kidney, thymus, prostate, ovary, intestine, colon, leukocytes,
liver; also HEV cells and cartilage.
[file:human/PAPSS1/PAPSS1-uniprot.txt "Expressed in testis, pancreas, kidney, thymus,"]

Notes on specific annotations

• GO:0001501 skeletal system development (TAS, PMID:9771708) — This reference is about the paralog
  PAPSS2 / ATPSK2 (the human SEMD and mouse brachymorphic gene), not PAPSS1. The paper maps SEMD to
  chromosome 10q23-24 and identifies mutations in ATPSK2/Atpsk2.
  PMID:9771708
  The skeletal/cartilage phenotype is the PAPSS2 (chondrocyte-restricted) function; PAPSS1 is broadly
  expressed. This is a non-experimental (TAS) annotation attributed to PAPSS1 but the cited paper does
  not concern PAPSS1 — treated as over-annotation / mis-attribution (kept non-core, flagged), not a
  core PAPSS1 function.

• GO:0005515 protein binding (IPI, PMID:33961781) — BioPlex 3.0 high-throughput AP-MS interactome;
  the with/from is PAPSS2 (O95340), consistent with UniProt's recorded PAPSS1–PAPSS2 IntAct interaction.
  Uninformative bare "protein binding" — marked over-annotated (per policy, IPI protein binding is not
  removed).

• GO:0042803 protein homodimerization activity (IPI, PMID:14747722) — supported by the homodimer
  observed in gel filtration and crystal structures. Real structural property; kept as non-core (the
  homodimer is the biological unit but the catalytic MFs are the core functions).

• GO:0016779 nucleotidyltransferase activity (ISS) — a less-specific parent of the ATP sulfurylase
  (sulfate adenylyltransferase) activity GO:0004781; MODIFY -> GO:0004781.

• Reactome cytosol annotations R-HSA-6802927/32/33/34/35 — these are "Signaling by BRAF and RAF1
  fusions" pathway reactions; the cytosol location is correct for PAPSS1 but the BRAF/RAF-fusion
  pathway context is spurious co-occurrence (PAPSS1 is not a component of RAF signaling). Location kept
  non-core.

Core functions (for review)

• MF: sulfate adenylyltransferase (ATP) activity — GO:0004781
• MF: adenylylsulfate kinase activity — GO:0004020
• MF: ATP binding — GO:0005524 (both catalytic reactions consume ATP; UniProt BINDING sites for two
  ATP molecules, labels 1 and 2)
• BP: sulfate assimilation — GO:0000103 / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process — GO:0050428
• CC: cytosol — GO:0005829; nucleus — GO:0005634