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PDBsum entry 1m7h

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1m7h
Jmol
Contents
Protein chains
203 a.a. *
Ligands
SO4 ×12
ADP ×4
ADX ×2
Waters ×499
* Residue conservation analysis
PDB id:
1m7h
Name: Transferase
Title: Crystal structure of aps kinase from penicillium chrysogenum: structure with aps soaked out of one dimer
Structure: Adenylylsulfate kinase. Chain: a, b, c, d. Synonym: aps kinase, adenosine-5'phosphosulfate kinase, atp adenosine-5'-phosphosulfate 3'- phosphotransferase. Engineered: yes
Source: Penicillium chrysogenum. Organism_taxid: 5076. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.215     R-free:   0.258
Authors: E.B.Lansdon,I.H.Sege,A.J.Fisher
Key ref:
E.B.Lansdon et al. (2002). Ligand-induced structural changes in adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum. Biochemistry, 41, 13672-13680. PubMed id: 12427029 DOI: 10.1021/bi026556b
Date:
19-Jul-02     Release date:   27-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q12657  (KAPS_PENCH) -  Adenylyl-sulfate kinase
Seq:
Struc:
211 a.a.
203 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.25  - Adenylyl-sulfate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
ATP
+
adenylyl sulfate
Bound ligand (Het Group name = ADX)
corresponds exactly
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ 3'-phosphoadenylyl sulfate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     hydrogen sulfide biosynthetic process   6 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi026556b Biochemistry 41:13672-13680 (2002)
PubMed id: 12427029  
 
 
Ligand-induced structural changes in adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum.
E.B.Lansdon, I.H.Segel, A.J.Fisher.
 
  ABSTRACT  
 
Adenosine 5'-phosphosulfate (APS) kinase catalyzes the second reaction in the two-step, ATP-dependent conversion of inorganic sulfate to 3'-phosphoadenosine 5'-phosphosulfate (PAPS). PAPS serves as the sulfuryl donor for the biosynthesis of all sulfate esters and also as a precursor of reduced sulfur biomolecules in many organisms. Previously, we determined the crystal structure of ligand-free APS kinase from the filamentous fungus, Penicillium chrysogenum [MacRae et al. (2000) Biochemistry 39, 1613-1621]. That structure contained a protease-susceptible disordered region ("mobile lid"; residues 145-170). Addition of MgADP and APS, which together promote the formation of a nonproductive "dead-end" ternary complex, protected the lid from trypsin. This report presents the 1.43 A resolution crystal structure of APS kinase with both ADP and APS bound at the active site and the 2.0 A resolution structure of the enzyme with ADP alone bound. The mobile lid is ordered in both complexes and is shown to provide part of the binding site for APS. That site is formed primarily by the highly conserved Arg 66, Arg 80, and Phe 75 from the protein core and Phe 165 from the mobile lid. The two Phe residues straddle the adenine ring of bound APS. Arg 148, a completely conserved residue, is the only residue in the mobile lid that interacts directly with bound ADP. Ser 34, located in the apex of the P-loop, hydrogen-bonds to the 3'-OH of APS, the phosphoryl transfer target. The structure of the binary E.ADP complex revealed further changes in the active site and N-terminal helix that occur upon the binding/release of (P)APS.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19770499 S.C.Gay, I.H.Segel, and A.J.Fisher (2009).
Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity.
  Acta Crystallogr D Biol Crystallogr, 65, 1021-1031.
PDB code: 3cr8
18423397 A.T.Torelli, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2008).
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
  Biochem Biophys Res Commun, 371, 154-158.
PDB code: 3cqs
17488874 A.T.Torelli, J.Krucinska, and J.E.Wedekind (2007).
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
  RNA, 13, 1052-1070.
PDB codes: 2p7d 2p7e 2p7f
17276460 N.Sekulic, K.Dietrich, I.Paarmann, S.Ort, M.Konrad, and A.Lavie (2007).
Elucidation of the active conformation of the APS-kinase domain of human PAPS synthetase 1.
  J Mol Biol, 367, 488-500.
PDB codes: 2ofw 2ofx
17540769 N.Sekulic, M.Konrad, and A.Lavie (2007).
Structural mechanism for substrate inhibition of the adenosine 5'-phosphosulfate kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 and its ramifications for enzyme regulation.
  J Biol Chem, 282, 22112-22121.
PDB codes: 2pey 2pez
17010373 J.Chartron, K.S.Carroll, C.Shiau, H.Gao, J.A.Leary, C.R.Bertozzi, and C.D.Stout (2006).
Substrate recognition, protein dynamics, and iron-sulfur cluster in Pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase.
  J Mol Biol, 364, 152-169.
PDB code: 2goy
16216072 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (2005).
Mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a CTP-inhibited complex.
  Biochemistry, 44, 13491-13499.
PDB code: 2ad5
15615729 M.Sun, J.L.Andreassi, S.Liu, R.Pinto, J.A.Triccas, and T.S.Leyh (2005).
The trifunctional sulfate-activating complex (SAC) of Mycobacterium tuberculosis.
  J Biol Chem, 280, 7861-7866.  
14613928 E.Hanna, K.F.Ng, I.J.MacRae, C.J.Bley, A.J.Fisher, and I.H.Segel (2004).
Kinetic and stability properties of Penicillium chrysogenum ATP sulfurylase missing the C-terminal regulatory domain.
  J Biol Chem, 279, 4415-4424.  
15157079 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (2004).
Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets.
  Biochemistry, 43, 6447-6463.
PDB code: 1s1m
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.