Structure for haloacid dehalogenase-like hydrolase domain containing 2: Difference between revisions

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   1: 3021-A 2ho4-A 43.4  0.0  246  246  100      0      0    1 S    HYDROLASE haloacid dehalogenase-like hydrolase domain  
   1: 3021-A 2ho4-A 43.4  0.0  246  246  100      0      0    1 S    HYDROLASE haloacid dehalogenase-like hydrolase domain  
   2: 3021-A 1pw5-A 24.3  2.9  230  246  25      0      0    17 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION nagd protein, pu
   2: 3021-A 1pw5-A 24.3  2.9  230  246  25      0      0    17 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION nagd protein, pu
  3: 3021-A 2hx1-A 16.9  4.7  224  275  23      0      0    30 S    HYDROLASE predicted sugar phosphatases of the had supe
  4: 3021-A 1qyi-A 13.7  3.0  150  375  21      0      0    15 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION hypothetical pro
   5: 3021-A 1o03-A 13.3  2.5  135  221  24      0      0    12 S    ISOMERASE beta-phosphoglucomutase (lactococcus lactis
   5: 3021-A 1o03-A 13.3  2.5  135  221  24      0      0    12 S    ISOMERASE beta-phosphoglucomutase (lactococcus lactis
  6: 3021-A 2gfh-A 12.9  2.4  131  246  19      0      0    14 S    HYDROLASE haloacid dehalogenase-like hydrolase domain
   7: 3021-A 1te2-A 12.8  2.4  133  211  17      0      0    15 S    HYDROLASE putative phosphatase (escherichia coli o157
   7: 3021-A 1te2-A 12.8  2.4  133  211  17      0      0    15 S    HYDROLASE putative phosphatase (escherichia coli o157
  8: 3021-A 1fez-A 12.6  2.2  134  256  16      0      0    18 S    HYDROLASE phosphonoacetaldehyde hydrolase (bacillus c
   9: 3021-A 1qq5-A 12.5  2.1  138  245  20      0      0    11 S    HYDROLASE l-2-haloacid dehalogenase (xanthobacter aut
   9: 3021-A 1qq5-A 12.5  2.1  138  245  20      0      0    11 S    HYDROLASE l-2-haloacid dehalogenase (xanthobacter aut
   10: 3021-A 2hsz-A 12.2  2.2  125  222  20      0      0    20 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION novel predicted  
   10: 3021-A 2hsz-A 12.2  2.2  125  222  20      0      0    20 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION novel predicted  

Revision as of 10:17, 5 June 2007

haloacid dehalogenase-like hydrolase

[| Sequence Details ]

[| Ideogram of HDHD2]

Pfam description (Accession number: PF00702)

This family are structurally different from the alpha/ beta hydrolase family (Abhydrolase_1). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSEUC. The rest of the fold is composed of the core alpha/beta domain.

N terminus = blue C terminus = red so the first 100 residues (aa's) should be in the blue region.

InterPro description (entry IPR005834)

This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase). This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain

Structure similarity Table (results from dali search)

number PDB code structural similarity (RMSD) (better if zero) seuqence identity (%IDE) (better if 100%) protein name comments
2 1pw5 2.9 25 STRUCTURAL GENOMICS, UNKNOWN FUNCTION, nagd protein, pu Could be a hydrolase, not sure
3 2hx1 4.7 23 HYDROLASE: predicted sugar phosphatases of the had superfamily The E. coli HAD phosphatases show high catalytic efficiency and affinity to a wide range of phosphorylated metabolites that are intermediates of various metabolic reactions. (pubmed)
5 1o03 2.5 24 ISOMERASE: beta-phosphoglucomutase (in lactococcus lactis) Phosphoglucomutases catalyze the interconversion of D-glucose 1-phosphate and D-glucose 6-phosphate, a reaction central to energy metabolism in all cells and to the synthesis of cell wall polysaccharides in bacterial cells. Two classes of phosphoglucomutases (alpha-PGM and beta-PGM) are distinguished on the basis of their specificity for alpha- and beta-glucose-1-phosphate. beta-PGM is a member of the haloacid dehalogenase (HAD) superfamily, which includes the sarcoplasmic Ca(2+)-ATPase, phosphomannomutase, and phosphoserine phosphatase. beta-PGM is unusual among family members in that the common phosphoenzyme intermediate exists as a stable ground-state complex in this enzyme. Herein we report, for the first time, the three-dimensional structure of a beta-PGM and the first view of the true phosphoenzyme intermediate in the HAD superfamily. (Pubmed)
22 2fpx 3.3 20 HYDROLASE: histidine biosynthesis bifunctional protein HisB from Escherichia coli is a bifunctional enzyme catalyzing the sixth and eighth steps of l-histidine biosynthesis. The N-terminal domain (HisB-N) possesses histidinol phosphate phosphatase activity, and its crystal structure shows a single domain with fold similarity to the haloacid dehalogenase (HAD) enzyme family. (Pubmed)
35 1f5s 3.1 23 HYDROLASE: phosphoserine phosphatase (psp) (in Methanococcus jannaschii) D-Serine is a co-agonist of the N-methyl-D-aspartate subtype of glutamate receptors, a major neurotransmitter receptor family in mammalian nervous systems. D-Serine is converted from L-serine, 90% of which is the product of the enzyme phosphoserine phosphatase (PSP). PSP from M. jannaschii (MJ) shares significant sequence homology with human PSP. PSPs and P-type ATPases are members of the haloacid dehalogenase (HAD)-like hydrolase family, and all members share three conserved sequence motifs. PSP and P-type ATPases utilize a common mechanism that involves Mg(2+)-dependent phosphorylation and autodephosphorylation at an aspartyl side chain in the active site (Abstract from PBD).
38 1j8d 3.0 19 HYDROLASE: deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679) The crystal structure of the YrbI protein from Haemophilus influenzae (HI1679) was determined at a 1.67-A resolution. The function of the protein had not been assigned previously, and it is annotated as hypothetical in sequence databases. The protein exhibits the alpha/beta-hydrolase fold (also termed the Rossmann fold) and resembles most closely the fold of the L-2-haloacid dehalogenase (HAD) superfamily. Following this observation, a detailed sequence analysis revealed remote homology to two members of the HAD superfamily, the P-domain of Ca(2+) ATPase and phosphoserine phosphatase (Abstract from PDM).

DALI server results

threshold Z > 9

FSSP FAMILIES OF STRUCTURALLY SIMILAR PROTEINS, VERSION 1.0 (Apr 1 1995) CREATED Tue May 8 05:22:07 BST 2007 for dali on s030-014.ebi.ac.uk METHOD Dali ver. 2.0: Holm, L., Sander, C. (1993) J.Mol.Biol. 233,123-138 DATABASE 8969 protein chains PDBID 3021-A HEADER COMPND SOURCE AUTHOR SEQLENGTH 246 NALIGN 242 WARNING pairs with Z<2.0 are structurally dissimilar

  NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
  1: 3021-A 2ho4-A 43.4  0.0  246   246  100      0      0     1 S    HYDROLASE 	haloacid dehalogenase-like hydrolase domain 
  2: 3021-A 1pw5-A 24.3  2.9  230   246   25      0      0    17 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	nagd protein, pu
  5: 3021-A 1o03-A 13.3  2.5  135   221   24      0      0    12 S    ISOMERASE 	beta-phosphoglucomutase 	(lactococcus lactis
  7: 3021-A 1te2-A 12.8  2.4  133   211   17      0      0    15 S    HYDROLASE 	putative phosphatase 	(escherichia coli o157
  9: 3021-A 1qq5-A 12.5  2.1  138   245   20      0      0    11 S    HYDROLASE 	l-2-haloacid dehalogenase 	(xanthobacter aut
 10: 3021-A 2hsz-A 12.2  2.2  125   222   20      0      0    20 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	novel predicted 
 11: 3021-A 1yns-A 11.6  2.2  127   254   14      0      0    17 S    HYDROLASE 	e-1 enzyme (enolase-phosphatase e1) 	(homo s
 12: 3021-A 2ah5-A 11.3  2.4  125   206   23      0      0    20 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	cog0546 	(strept
 13: 3021-A 1wdh-A 11.2  2.2  125   248   14      0      0    17 S    
 14: 3021-A 2p11-A 10.4  2.4  130   211   18      0      0    15 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	hypothetical pro
 15: 3021-A 1rku-A 10.4  2.9  132   206   14      0      0    15 S    TRANSFERASE 	homoserine kinase 	(pseudomonas aeruginosa
 16: 3021-A 2go7-A 10.3  2.5  120   203   25      0      0    15 S    HYDROLASE 	hydrolase, haloacid dehalogenase-like family
 17: 3021-A 2fdr-A 10.3  2.3  128   214   20      0      0    17 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	conserved hypoth
 18: 3021-A 1ymq-A 10.2  3.7  163   260   17      0      0    22 S    TRANSFERASE 	sugar-phosphate phosphatase bt4131 	(bacte
 19: 3021-A 2fi1-A 10.0  2.4  112   187   22      0      0    14 S    HYDROLASE 	hydrolase, haloacid dehalogenase-like family
 20: 3021-A 1rlm-A 10.0  3.2  146   269   12      0      0    21 S    HYDROLASE 	phosphatase Mutant 	(escherichia coli) bacte


Literature to read

[| YbiV from Escherichia coli K12 is a HAD phosphatase.]


The protein is comrprised of 2 Biological units.

Biological Unit 1
Biological Unit 2

The Whole protein comprised of both compounds.

Whole protein with both units