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PDBsum entry 1pwh

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1pwh
Jmol
Contents
Protein chains
327 a.a. *
Ligands
PLV ×4
Metals
__K ×4
Waters ×119
* Residue conservation analysis
PDB id:
1pwh
Name: Lyase
Title: Rat liver l-serine dehydratase- complex with pyridoxyl-(o- methyl-serine)-5-monophosphate
Structure: L-serine dehydratase. Chain: a, b, c, d. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.230     R-free:   0.260
Authors: T.Yamada,J.Komoto,Y.Takata,H.Ogawa,F.Takusagawa
Key ref:
T.Yamada et al. (2003). Crystal structure of serine dehydratase from rat liver. Biochemistry, 42, 12854-12865. PubMed id: 14596599 DOI: 10.1021/bi035324p
Date:
01-Jul-03     Release date:   02-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09367  (SDHL_RAT) -  L-serine dehydratase/L-threonine deaminase
Seq:
Struc:
363 a.a.
327 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.4.3.1.17  - L-serine ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-serine = pyruvate + NH3
L-serine
= pyruvate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate or iron-sulfur
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLV) matches with 62.00% similarity
or iron-sulfur
   Enzyme class 2: E.C.4.3.1.19  - Threonine ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: L-threonine = 2-oxobutanoate + NH3
L-threonine
= 2-oxobutanoate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate or iron-sulfur
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLV) matches with 62.00% similarity
or iron-sulfur
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   2 terms 
  Biological process     response to nutrient levels   5 terms 
  Biochemical function     lyase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi035324p Biochemistry 42:12854-12865 (2003)
PubMed id: 14596599  
 
 
Crystal structure of serine dehydratase from rat liver.
T.Yamada, J.Komoto, Y.Takata, H.Ogawa, H.C.Pitot, F.Takusagawa.
 
  ABSTRACT  
 
SDH (L-serine dehydratase, EC 4.3.1.17) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent dehydration of L-serine to yield pyruvate and ammonia. Liver SDH plays an important role in gluconeogenesis. Formation of pyruvate by SDH is a two-step reaction in which the hydroxyl group of serine is cleaved to produce aminoacrylate, and then the aminoacrylate is deaminated by nonenzymatic hydrolysis to produce pyruvate. The crystal structure of rat liver apo-SDH was determined by single isomorphous replacement at 2.8 A resolution. The holo-SDH crystallized with O-methylserine (OMS) was also determined at 2.6 A resolution by molecular replacement. SDH is composed of two domains, and each domain has a typical alphabeta-open structure. The active site is located in the cleft between the two domains. The holo-SDH contained PLP-OMS aldimine in the active site, indicating that OMS can form the Schiff base linkage with PLP, but the subsequent dehydration did not occur. Apo-SDH forms a dimer by inserting the small domain into the catalytic cleft of the partner subunit so that the active site is closed. Holo-SDH also forms a dimer by making contacts at the back of the clefts so that the dimerization does not close the catalytic cleft. The phosphate group of PLP is surrounded by a characteristic G-rich sequence ((168)GGGGL(172)) and forms hydrogen bonds with the amide groups of those amino acid residues, suggesting that the phosphate group can be protonated. N(1) of PLP participates in a hydrogen bond with Cys303, and similar hydrogen bonds with N(1) participating are seen in other beta-elimination enzymes. These hydrogen bonding schemes indicate that N(1) is not protonated, and thus, the pyridine ring cannot take a quinone-like structure. These characteristics of the bound PLP suggest that SDH catalysis is not facilitated by forming the resonance-stabilized structure of the PLP-Ser aldimine as seen in aminotransferases. A possible catalytic mechanism involves the phosphate group, surrounded by the characteristic sequence, acting as a general acid to donate a proton to the leaving hydroxyl group of serine.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944214 G.W.Han, C.Bakolitsa, M.D.Miller, A.Kumar, D.Carlton, R.J.Najmanovich, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, D.Ernst, J.Feuerhelm, J.C.Grant, A.Grzechnik, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1218-1225.
PDB codes: 2ra9 2re3
20370823 K.Nishio, K.Ogasahara, Y.Morimoto, T.Tsukihara, S.J.Lee, and K.Yutani (2010).
Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.
  FEBS J, 277, 2157-2170.
PDB codes: 2dh5 2dh6
19640845 M.Goto, T.Yamauchi, N.Kamiya, I.Miyahara, T.Yoshimura, H.Mihara, T.Kurihara, K.Hirotsu, and N.Esaki (2009).
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
  J Biol Chem, 284, 25944-25952.
PDB codes: 1wtc 2zr8
19402712 P.D.Cook, R.L.Kubiak, D.P.Toomey, and H.M.Holden (2009).
Two site-directed mutations are required for the conversion of a sugar dehydratase into an aminotransferase.
  Biochemistry, 48, 5246-5253.
PDB code: 3gr9
18931110 N.J.Zelyas, H.Cai, T.Kwong, and S.E.Jensen (2008).
Alanylclavam biosynthetic genes are clustered together with one group of clavulanic acid biosynthetic genes in Streptomyces clavuligerus.
  J Bacteriol, 190, 7957-7965.  
18564179 T.Yoshimura, and M.Goto (2008).
D-amino acids in the brain: structure and function of pyridoxal phosphate-dependent amino acid racemases.
  FEBS J, 275, 3527-3537.  
17954980 D.K.Simanshu, S.Chittori, H.S.Savithri, and M.R.Murthy (2007).
Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate.
  J Biosci, 32, 1195-1206.  
17766369 F.N.Musayev, M.L.di Salvo, T.P.Ko, A.K.Gandhi, A.Goswami, V.Schirch, and M.K.Safo (2007).
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
  Protein Sci, 16, 2184-2194.
PDB codes: 2yxt 2yxu
17407165 K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.
  Proteins, 68, 109-122.  
17046821 D.K.Simanshu, H.S.Savithri, and M.R.Murthy (2006).
Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.
  J Biol Chem, 281, 39630-39641.
PDB codes: 2gn0 2gn1 2gn2
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
17001724 F.P.Seebeck, A.Guainazzi, C.Amoreira, K.K.Baldridge, and D.Hilvert (2006).
Stereoselectivity and expanded substrate scope of an engineered PLP-dependent aldolase.
  Angew Chem Int Ed Engl, 45, 6824-6826.  
15757516 A.J.Edgar (2005).
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.
  BMC Genomics, 6, 32.  
16166087 E.R.Bonner, R.E.Cahoon, S.M.Knapke, and J.M.Jez (2005).
Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana.
  J Biol Chem, 280, 38803-38813.
PDB codes: 1z7w 1z7y
15689518 L.Sun, M.Bartlam, Y.Liu, H.Pang, and Z.Rao (2005).
Crystal structure of the pyridoxal-5'-phosphate-dependent serine dehydratase from human liver.
  Protein Sci, 14, 791-798.  
15618015 T.Kashii, T.Gomi, T.Oya, Y.Ishii, H.Oda, M.Maruyama, M.Kobayashi, T.Masuda, M.Yamazaki, T.Nagata, K.Tsukada, A.Nakajima, K.Tatsu, H.Mori, F.Takusagawa, H.Ogawa, and H.C.Pitot (2005).
Some biochemical and histochemical properties of human liver serine dehydratase.
  Int J Biochem Cell Biol, 37, 574-589.  
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 codes are shown on the right.