PDBsum entry 1dd2

Transferase

PDB id

1dd2

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Contents

			Protein chain

					77 a.a. *

* Residue conservation analysis

PDB id:

1dd2

Links

Name:

Transferase

Title:

Biotin carboxyl carrier domain of transcarboxylase (tc 1.3s)

Structure:

Transcarboxylase 1.3s subunit. Chain: a. Engineered: yes

Source:

Propionibacterium freudenreichii subsp. Shermanii. Organism_taxid: 1752. Strain: subsp. Shermanii. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

32 models

Authors:

D.V.Reddy,B.C.Shenoy,P.R.Carey,F.D.Sonnichsen

Key ref:

D.V.Reddy et al. (2000). High resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii. Biochemistry, 39, 2509-2516. PubMed id: 10704200 DOI: 10.1021/bi9925367

Date:

06-Nov-99

Release date:

24-Mar-00

PROCHECK

	Headers

	References

Protein chain

P02904 (BCCP_PROFR) - Methylmalonyl-CoA carboxyltransferase 1.3S subunit from Propionibacterium freudenreichii subsp. shermanii

Seq: Struc:					123 a.a. 77 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.1.3.1 - methylmalonyl-CoA carboxytransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

(S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate

(S)-methylmalonyl-CoA	+	pyruvate	=	propanoyl-CoA	+	oxaloacetate

Cofactor:

Biotin; Cobalt cation; Zn(2+)

Biotin	Cobalt cation	Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi9925367	Biochemistry 39:2509-2516 (2000)
PubMed id: 10704200

High resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii.
D.V.Reddy, B.C.Shenoy, P.R.Carey, F.D.Sönnichsen.

ABSTRACT

Transcarboxylase (TC) from Propionibacterium shermanii, a biotin-dependent enzyme, catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate to form propionyl-CoA and oxalacetate. Within the multi-subunit enzyme complex, the 1.3S subunit functions as the carboxyl group carrier and also binds the other two subunits to assist in the overall assembly of the enzyme. The 1.3S subunit is a 123 amino acid polypeptide (12.6 kDa) to which biotin is covalently attached at Lys 89. The three-dimensional solution structure of the full-length holo-1.3S subunit of TC has been solved by multidimensional heteronuclear NMR spectroscopy. The C-terminal half of the protein (51-123) is folded into a compact all-beta-domain comprising of two four-stranded antiparallel beta-sheets connected by short loops and turns. The fold exhibits a high 2-fold internal symmetry and is similar to that of the biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase, but lacks an extension that has been termed "protruding thumb" in BCCP. The first 50 residues, which have been shown to be involved in intersubunit interactions in the intact enzyme, appear to be disordered in the isolated 1.3S subunit. The molecular surface of the folded domain has two distinct surfaces: one side is highly charged, while the other comprises mainly hydrophobic, highly conserved residues.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21204864

G.Gago, L.Diacovich, A.Arabolaza, S.C.Tsai, and H.Gramajo (2011).
Fatty acid biosynthesis in actinomycetes.

FEMS Microbiol Rev, 35, 475-497.

19284579

J.E.Butler, N.D.Young, and D.R.Lovley (2009).
Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.

BMC Genomics, 10, 103.

18372281

B.Bagautdinov, Y.Matsuura, S.Bagautdinova, and N.Kunishima (2008).
Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate.

J Biol Chem, 283, 14739-14750.

PDB codes:

1x01 2d5d 2dxu 2dzc 2e41 2e64 2ejf 2ejg 2evb 2zgw

18247344

C.K.Lee, H.K.Cheong, K.S.Ryu, J.I.Lee, W.Lee, Y.H.Jeon, and C.Cheong (2008).
Biotinoyl domain of human acetyl-CoA carboxylase: Structural insights into the carboxyl transfer mechanism.

Proteins, 72, 613-624.

PDB code:

2kcc

17472384

I.Chen, Y.A.Choi, and A.Y.Ting (2007).
Phage display evolution of a peptide substrate for yeast biotin ligase and application to two-color quantum dot labeling of cell surface proteins.

J Am Chem Soc, 129, 6619-6625.

17893191

N.M.Lorenzon, and K.G.Beam (2007).
Accessibility of targeted DHPR sites to streptavidin and functional effects of binding on EC coupling.

J Gen Physiol, 130, 379-388.

17584037

S.K.Campos, and M.A.Barry (2007).
Current advances and future challenges in Adenoviral vector biology and targeting.

Curr Gene Ther, 7, 189-204.

16823034

E.D.Streaker, and D.Beckett (2006).
Nonenzymatic biotinylation of a biotin carboxyl carrier protein: unusual reactivity of the physiological target lysine.

Protein Sci, 15, 1928-1935.

16699181

G.Cui, B.Nan, J.Hu, Y.Wang, C.Jin, and B.Xia (2006).
Identification and solution structures of a single domain biotin/lipoyl attachment protein from Bacillus subtilis.

J Biol Chem, 281, 20598-20607.

PDB code:

1z6h

16627940

Y.Maegawa, H.Morita, D.Iyaguchi, M.Yao, N.Watanabe, and I.Tanaka (2006).
Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.

Acta Crystallogr D Biol Crystallogr, 62, 483-488.

PDB code:

1vdz

15459338

E.Choi-Rhee, H.Schulman, and J.E.Cronan (2004).
Promiscuous protein biotinylation by Escherichia coli biotin protein ligase.

Protein Sci, 13, 3043-3050.

15280388

N.M.Lorenzon, C.S.Haarmann, E.E.Norris, S.Papadopoulos, and K.G.Beam (2004).
Metabolic biotinylation as a probe of supramolecular structure of the triad junction in skeletal muscle.

J Biol Chem, 279, 44057-44064.

14993680

P.R.Hall, R.Zheng, M.Pusztai-Carey, F.van den Akker, P.R.Carey, and V.C.Yee (2004).
Expression and crystallization of several forms of the Propionibacterium shermanii transcarboxylase 5S subunit.

Acta Crystallogr D Biol Crystallogr, 60, 521-523.

15610612

S.K.Campos, and M.A.Barry (2004).
Rapid construction of capsid-modified adenoviral vectors through bacteriophage lambda Red recombination.

Hum Gene Ther, 15, 1125-1130.

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

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

11956202

J.E.Cronan (2002).
Interchangeable enzyme modules. Functional replacement of the essential linker of the biotinylated subunit of acetyl-CoA carboxylase with a linker from the lipoylated subunit of pyruvate dehydrogenase.

J Biol Chem, 277, 22520-22527.

12121720

J.E.Cronan, and G.L.Waldrop (2002).
Multi-subunit acetyl-CoA carboxylases.

Prog Lipid Res, 41, 407-435.

11173475

Y.F.Wang, D.C.Hyatt, R.E.Rivera, P.R.Carey, and V.C.Yee (2001).
Crystallization and preliminary X-ray analysis of the 12S central subunit of transcarboxylase from Propionibacterium shermanii.

Acta Crystallogr D Biol Crystallogr, 57, 266-268.

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.