Dihydrodipicolinate synthase

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CRYSTAL STRUCTURE OF YAGE, A PROPHAGE PROTEIN BELONGING TO THE DIHYDRODIPICOLINIC ACID SYNTHASE FAMILY FROM E. COLI K12

One approach of the incorporation of genetic material from different species into bacterial genomes is infection by a bacteriophage. The yagE gene is located in the E. coli K12 genome and it is part of prophage CP4-6 encoding a 33-kDa putative dihydrodipicolinate synthase (DHDPS)-like protein (UniProtKB/Swiss-prot: P75682). This DHDPS-like domain is a member of the N-acetyl neuraminate lyase (NAL) subfamily comprises an 8-fold (TIM barrel) with a small C-terminal α-helical domain (Inter pro: IPR005263). Many enzymes possess this DHDPS domain (e.g. HBPHA, KDGA, NAL, DOGDH, and DHDPS). All these enzymes contain an 8-fold α/β barrel and a small C-terminal α-helical region. between orthorhombic (2v8z) and monoclinic (2v9d) crystal forms of YagE revealed striking similarity.

Cartoon representation of YagE showing the 2-fold symmetry axes between monomers. Chains A, B, C, and D are colored cyan, lime, magenta, and yellow, respectively. of YagE (cyan) with (1nal, yellow), (1w3i, magenta), (1xky, lime), and (2ats, blue) monomers. Although YagE possesses only 23, 24, and 27% sequence identity with EcNAL, SsKDGA, EcDHDPS, respectively, their monomeric structures are all very similar. Superposition of active site residues of YagE with (magenta, 1w3i), (blue, 2ats), and (yellow, 1nal), residues are labeled according to the corresponding PDB structures. Members of the NAL protein subfamily have very similar active sites and a single amino acid substitution can significantly change their function. For example, NAL (1nal) gets DHDPS activity by substitution of a (orange) to (blue) at position 142. The possible active site region of YagE demonstrates closest sequence similarity to the active site of KDG aldolase of SsKDGA (1w3i) and NAL of EcNAL (1nal) (yellow), suggesting that this protein can perform either of these functions. Although the active site of EcDHDPS (1xky) and BaDHDPS (2ats) shows similarities, the important residue that differentiates between NAL and DHDPS, namely Leu142 (in 1nal), is also present in YagE (labeled cyan) at that particular position suggesting that YagE performs a NAL-related function rather than DHDPS-related one. In conclusion, the high-resolution X-ray structure of YagE provides a clue that it probably belongs to the NAL subfamily of proteins. Although the exact molecular function of YagE is still unknown, its structure provides a handle for understanding its molecular function based on knowledge about conserved residues of the putative active site.

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3D structures of dihydrodipicolinate synthase3D structures of dihydrodipicolinate synthase

Updated on 20-July-2014

1dhp, 1s5t, 1s5v, 1s5w, 2a6l, 2a6n, 2ojp, 2pur, 3den, 3i7q, 3i7r – EcDPS (mutant) – Escherichia coli
1yxc - EcDPS
1o5k – TmDPS – Thermotoga maritima
3pb0, 3pb2 – TmDPS (mutant)
1xky, 1xl9 – BaDPS – Bacillus anthracis
1xxx – MtDPS – Mycobacterium tuberculosis
3l21 – MtDPS (mutant)
2hmc, 2r8w, 3b4u, 4i7u, 4i7v – DPS – Agrobacterium tumdefaciens
2ehh – DPS – Aquifex aeolicus
2rfg – DPS – Hahella chejuensis
2yxg – DPS – Methanocaldococcus jannaschii
3d0c – DPS – Oceanobacillus iheyensis
3daq, 3di0 – SaDPS – Staphylococcus aureus
3dz1 – DPS – Rhodopseudomonas palustris
3e96 – DPS – Bacillus clausii
3cpr – DPS – Corynebacterium glutamicum
3g0s – DPS – Salmonella typhimurium
3flu – DPS – Neisseria meningitides
3ird, 3a5f – DPS – Clostridium botulinum
3h5d, 3vfl – SpDPS – Streptococcus pneumoniae
3ler, 3m5v – DPS – Campylobacter jejuni
3noe, 3ps7, 3qze – PaDPS – Psuedomonas aeruginosa
3pud, 3pul, 4dxv – AbDPS – Acinetobacter baumannii
3si9 – DSP – Bartonella henselae
4dpp – AtDPS – Arabidopsis thaliana
3tuu – grDPS – grapevine
4icn - DPS – Shewanella benthica

DPS binary complexesDPS binary complexes

1yxd, 2ats – EcDPS + S-Lys
4dpq - AtDPS + S-Lys
3pue - AbDPS + Lys
3tce - AbDPS + hydroxylysine
3tdf - AbDPS + ketobutanoic acid
3u8g - AbDPS + oxalic acid
3uqn - AbDPS + oxamic acid
3puo - PaDPS + Lys
4fha - SpDPS + Lys
4hnn - grDPS + Lys
4i7w - AtDPS + Lys
2vc6 – DPS + pyruvate – Sinorhizobium meliloti
3di1 - SaDPS + pyruvate
3c0j - EcDPS + hydroxypyruvate
3du0 - EcDPS + pyruvate
3i7s - EcDPS (mutant) + pyruvate
4eou - EcDPS + succinic semialdehyde
3hij - BaDPS + pyruvate
3rk8, 3tak - AbDPS + pyruvate
3s8h - PaDPS + hydroxypropanoic acid

ReferenceReference

Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12., Manicka S, Peleg Y, Unger T, Albeck S, Dym O, Greenblatt HM, Bourenkov G, Lamzin V, Krishnaswamy S, Sussman JL, Proteins. 2008 Jun;71(4):2102-8. PMID:18361457

• Created with the participation of Jaime Prilusky and Michal Harel.