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PDBsum entry 1ef8
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protein metals Protein-protein interface(s) links
Lyase PDB id
1ef8

 

 

 

 

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Contents
Protein chains
256 a.a. *
Metals
_NI
Waters ×603
* Residue conservation analysis
PDB id:
1ef8
Name: Lyase
Title: Crystal structure of methylmalonyl coa decarboxylase
Structure: Methylmalonyl coa decarboxylase. Chain: a, b, c. Ec: 4.1.1.41
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
1.85Å     R-factor:   0.180     R-free:   0.237
Authors: M.M.Benning,T.Haller,J.A.Gerlt,H.M.Holden
Key ref:
M.M.Benning et al. (2000). New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli. Biochemistry, 39, 4630-4639. PubMed id: 10769118 DOI: 10.1021/bi9928896
Date:
07-Feb-00     Release date:   24-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52045  (SCPB_ECOLI) -  Methylmalonyl-CoA decarboxylase from Escherichia coli (strain K12)
Seq:
Struc: 		261 a.a.
256 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/bi9928896 Biochemistry 39:4630-4639 (2000)
PubMed id: 10769118  
 
 
New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.
M.M.Benning, T.Haller, J.A.Gerlt, H.M.Holden.
 
  ABSTRACT  
 
The molecular structure of methylmalonyl CoA decarboxylase (MMCD), a newly defined member of the crotonase superfamily encoded by the Escherichia coli genome, has been solved by X-ray crystallographic analyses to a resolution of 1.85 A for the unliganded form and to a resolution of 2.7 A for a complex with an inert thioether analogue of methylmalonyl CoA. Like two other structurally characterized members of the crotonase superfamily (crotonase and dienoyl CoA isomerase), MMCD is a hexamer (dimer of trimers) with each polypeptide chain composed of two structural motifs. The larger N-terminal domain contains the active site while the smaller C-terminal motif is alpha-helical and involved primarily in trimerization. Unlike the other members of the crotonase superfamily, however, the C-terminal motif is folded back onto the N-terminal domain such that each active site is wholly contained within a single subunit. The carboxylate group of the thioether analogue of methylmalonyl CoA is hydrogen bonded to the peptidic NH group of Gly 110 and the imidazole ring of His 66. From modeling studies, it appears that Tyr 140 is positioned within the active site to participate in the decarboxylation reaction by orienting the carboxylate group of methylmalonyl CoA so that it is orthogonal to the plane of the thioester carbonyl group. Surprisingly, while the active site of MMCD contains Glu 113, which is homologous to the general acid/base Glu 144 in the active site of crotonase, its carboxylate side chain is hydrogen bonded to Arg 86, suggesting that it is not directly involved in catalysis. The new constellation of putative functional groups observed in the active site of MMCD underscores the diversity of function in this superfamily.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20300652 D.E.Almonacid, E.R.Yera, J.B.Mitchell, and P.C.Babbitt (2010).
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
  PLoS Comput Biol, 6, e1000700.  
20199672 E.Cilia, and A.Passerini (2010).
Automatic prediction of catalytic residues by modeling residue structural neighborhood.
  BMC Bioinformatics, 11, 115.  
20826333 L.Chen (2010).
Signal synthesis for a rapid response.
  Structure, 18, 1072-1073.  
20826346 Z.Cheng, Y.W.He, S.C.Lim, R.Qamra, M.A.Walsh, L.H.Zhang, and H.Song (2010).
Structural basis of the sensor-synthase interaction in autoinduction of the quorum sensing signal DSF biosynthesis.
  Structure, 18, 1199-1209.
PDB codes: 3m6m 3m6n
19369256 J.Bains, R.Leon, and M.J.Boulanger (2009).
Structural and Biophysical Characterization of BoxC from Burkholderia xenovorans LB400: A NOVEL RING-CLEAVING ENZYME IN THE CROTONASE SUPERFAMILY.
  J Biol Chem, 284, 16377-16385.
PDB code: 2w3p
18831052 K.Kurimoto, K.Kuwasako, A.M.Sandercock, S.Unzai, C.V.Robinson, Y.Muto, and S.Yokoyama (2009).
AU-rich RNA-binding induces changes in the quaternary structure of AUH.
  Proteins, 75, 360-372.
PDB codes: 2zqq 2zqr
19533699 P.F.Widboom, and S.D.Bruner (2009).
Complex oxidation chemistry in the biosynthetic pathways to vancomycin/teicoplanin antibiotics.
  Chembiochem, 10, 1757-1764.  
19016856 G.Meriläinen, W.Schmitz, R.K.Wierenga, and P.Kursula (2008).
The sulfur atoms of the substrate CoA and the catalytic cysteine are required for a productive mode of substrate binding in bacterial biosynthetic thiolase, a thioester-dependent enzyme.
  FEBS J, 275, 6136-6148.
PDB codes: 2vtz 2vu0 2vu1 2vu2
17928301 T.W.Geders, L.Gu, J.C.Mowers, H.Liu, W.H.Gerwick, K.Håkansson, D.H.Sherman, and J.L.Smith (2007).
Crystal structure of the ECH2 catalytic domain of CurF from Lyngbya majuscula. Insights into a decarboxylase involved in polyketide chain beta-branching.
  J Biol Chem, 282, 35954-35963.
PDB codes: 2q2x 2q34 2q35
16757561 C.T.Calderone, W.E.Kowtoniuk, N.L.Kelleher, C.T.Walsh, and P.C.Dorrestein (2006).
Convergence of isoprene and polyketide biosynthetic machinery: isoprenyl-S-carrier proteins in the pksX pathway of Bacillus subtilis.
  Proc Natl Acad Sci U S A, 103, 8977-8982.  
17139085 P.M.Leonard, A.M.Brzozowski, A.Lebedev, C.M.Marshall, D.J.Smith, C.S.Verma, N.J.Walton, and G.Grogan (2006).
The 1.8 A resolution structure of hydroxycinnamoyl-coenzyme A hydratase-lyase (HCHL) from Pseudomonas fluorescens, an enzyme that catalyses the transformation of feruloyl-coenzyme A to vanillin.
  Acta Crystallogr D Biol Crystallogr, 62, 1494-1501.
PDB code: 2j5i
16131752 J.M.Johnston, V.L.Arcus, and E.N.Baker (2005).
Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms.
  Acta Crystallogr D Biol Crystallogr, 61, 1199-1206.  
16096274 M.C.Sleeman, J.L.Sorensen, E.T.Batchelar, M.A.McDonough, and C.J.Schofield (2005).
Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis.
  J Biol Chem, 280, 34956-34965.
PDB codes: 2a7k 2a81
16113715 N.J.Kershaw, M.E.Caines, M.C.Sleeman, and C.J.Schofield (2005).
The enzymology of clavam and carbapenem biosynthesis.
  Chem Commun (Camb), (), 4251-4263.  
15883186 P.A.Hubbard, W.Yu, H.Schulz, and J.J.Kim (2005).
Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase.
  Protein Sci, 14, 1545-1555.
PDB code: 1xx4
16151134 R.Chakraborty, and J.D.Coates (2005).
Hydroxylation and carboxylation--two crucial steps of anaerobic benzene degradation by Dechloromonas strain RCB.
  Appl Environ Microbiol, 71, 5427-5432.  
14625287 M.C.Sleeman, and C.J.Schofield (2004).
Carboxymethylproline synthase (CarB), an unusual carbon-carbon bond-forming enzyme of the crotonase superfamily involved in carbapenem biosynthesis.
  J Biol Chem, 279, 6730-6736.  
15138275 P.M.Leonard, and G.Grogan (2004).
Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-alpha-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog.
  J Biol Chem, 279, 31312-31317.
PDB code: 1szo
14506256 G.J.Poelarends, W.H.Johnson, A.G.Murzin, and C.P.Whitman (2003).
Mechanistic characterization of a bacterial malonate semialdehyde decarboxylase: identification of a new activity on the tautomerase superfamily.
  J Biol Chem, 278, 48674-48683.  
12663926 H.Zhang, Z.Yang, Y.Shen, and L.Tong (2003).
Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase.
  Science, 299, 2064-2067.
PDB codes: 1od2 1od4
12909628 J.J.Truglio, K.Theis, Y.Feng, R.Gajda, C.Machutta, P.J.Tonge, and C.Kisker (2003).
Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis.
  J Biol Chem, 278, 42352-42360.
PDB codes: 1q51 1q52
12697341 J.K.Hiltunen, A.M.Mursula, H.Rottensteiner, R.K.Wierenga, A.J.Kastaniotis, and A.Gurvitz (2003).
The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces cerevisiae.
  FEMS Microbiol Rev, 27, 35-64.  
12421807 J.L.Whittingham, J.P.Turkenburg, C.S.Verma, M.A.Walsh, and G.Grogan (2003).
The 2-A crystal structure of 6-oxo camphor hydrolase. New structural diversity in the crotonase superfamily.
  J Biol Chem, 278, 1744-1750.
PDB code: 1o8u
12853465 K.S.Wendt, I.Schall, R.Huber, W.Buckel, and U.Jacob (2003).
Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
  EMBO J, 22, 3493-3502.
PDB code: 1pix
12615898 L.Lu, J.Vollmer, C.Moulon, H.U.Weltzien, P.Marrack, and J.Kappler (2003).
Components of the ligand for a Ni++ reactive human T cell clone.
  J Exp Med, 197, 567-574.  
12743028 P.R.Hall, Y.F.Wang, R.E.Rivera-Hainaj, X.Zheng, M.Pustai-Carey, P.R.Carey, and V.C.Yee (2003).
Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core.
  EMBO J, 22, 2334-2347.
PDB codes: 1on3 1on9
11327833 A.F.Bell, J.Wu, Y.Feng, and P.J.Tonge (2001).
Involvement of glycine 141 in substrate activation by enoyl-CoA hydratase.
  Biochemistry, 40, 1725-1733.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11738050 K.Kurimoto, S.Fukai, O.Nureki, Y.Muto, and S.Yokoyama (2001).
Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase.
  Structure, 9, 1253-1263.
PDB code: 1hzd
  11178260 J.A.Gerlt, and P.C.Babbitt (2000).
Can sequence determine function?
  Genome Biol, 1, REVIEWS0005.  
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.

 

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