Chitinase-like lectins - sequence alignment

Alignment of chitinase-like (glycoside hydrolase family 18) domains in human and mouse proteins.  Regions of secondary structure are indicated above the alignment and coloured to correspond with the structure of Ym1, left.  Alpha helices in the TIM-like domain (a1-8) and the small alpha/beta domain (aC) are higlighted in red.  Beta sheets in the TIM-like domain (b1-8) are highlighted in blue and those in the small alpha/beta domain (bA-B, bD-F) in yellow. 

Residues that are identical in over 75% of the aligned sequences are highlighted in green.  Residues that are similar in over 75% of the sequences are highlighted in cyan.  Cysteine residues which form disulfide bonds are highlighted in yellow.  with disulfide pairings numbered 1 and 2.  Residues from the active site motif DXXDXDXE, which includes the catalytic glutamate residue, are highlighted in magenta where identical to the motif and in pink where similar. 

Side chains in human YKL-40 which make hydrogen bonds to bound chito-oligosaccharides, and the conserved equivalents in other proteins, are highlighted in red.  Hydrophobic residue of the substrate binding cleft, and the conserved equivalents in other proteins, are highlighted in orange. Residues making both hydrogen bonds and hydrophobic interactions are marked x.  Conservation of hydrophobic residues in YKL-40 and active chitinases, but not in Ym1, may account for differences in ligand binding specificity.

 

Accession numbers

HS = human MM = mouse

LOC149620 HS Q5VUV6

AMCase HS Q5VUV4 Q3B866 Q5VUV3 Q5VUV5 Q5U5Z5 Q9BZP6 Q32W80 Q32W79 Q2VT96 MM Q91XA9

CHIT1 HS Q13231 Q3ZAR1 Q6ISC2 Q9UDJ8 Q6ZNK1 MM Q9D7Q1 Q6QJD2

Ym1 MM O35744 Q61201 Q3UV87 Q3U462  Ym2 MM Q91Z98 Q3V2C9

BCLP1/2 MM  Q8CJF6 Q8CJF5  LOC229688 MM Q80W26

YKL39 HS Q15782 Q96F97 Q53FH2 Q5VUV7

YKL40 HS P36222 MM Q61362 Q4FJW9 Q3U291

OVGP HS Q12889 Q86YN0 Q59HH5 MM Q62010 Q8C6P2 Q5GJ02 Q54AJ4 Q99MJ5

DIAC HS Q01459 Q5VX50 Q5VX51 MM Q8R242

CHID1 HS Q9BY52 Q9BWS9 Q96CZ3 Q96S93 Q8NBM9 Q96SK0 MM Q3TVF7 Q922Q9 Q6P8U4 Q8C7C5 Q9CRU8 Q9CXR7

 

Structure of murine Ym1

Beta-strands in the TIM domain are shown in light blue and those in the small insertion domain in yellow.  The modelled glucosamine molecule is shown in dark blue.  Protein Data Bank structure ID: 1E9L.