Structure of N-acetylneuraminic acid phosphatase

Chain Sequence

MGSDKIHHHHHHMGLSRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYSTCI TDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQ SYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKSGRVPLTSSPMPHYMVS SVLELPALLQSIDCKVSMSV

structure 18

DALI Search Results

SUMMARY: PDB/chain identifiers and structural alignment statistics
NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
 1: 3033-A 2gfh-A 41.1  0.0  246   246  100      0      0     1 S    HYDROLASE        haloacid dehalogenase-like hydrolase domain
 2: 3033-A 1fez-A 18.1  3.5  178   256   22      0      0    13 S    HYDROLASE        phosphonoacetaldehyde hydrolase         (bacillus c 
 3: 3033-A 2hsz-A 17.9  3.3  168   222   23      0      0    13 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    novel predicted
 4: 3033-A 1qq5-A 17.3  3.1  198   245   19      0      0    12 S    HYDROLASE        l-2-haloacid dehalogenase       (xanthobacter aut 
 5: 3033-A 1o03-A 17.0  5.0  188   221   20      0      0    11 S    ISOMERASE        beta-phosphoglucomutase         (lactococcus lactis
 6: 3033-A 2b0c-A 16.4  2.6  184   199   20      0      0    13 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    putative phospha 
 7: 3033-A 2fdr-A 15.8  4.4  190   214   19      0      0    15 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    conserved hypoth
 8: 3033-A 2p11-A 15.7  2.9  194   211   16      0      0    20 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    hypothetical pro 
 9: 3033-A 1te2-A 15.7  3.6  170   211   19      0      0    15 S    HYDROLASE        putative phosphatase    (escherichia coli o157
10: 3033-A 1yns-A 15.3  4.0  169   254   11      0      0    13 S    HYDROLASE        e-1 enzyme (enolase-phosphatase e1)     (homo s 
11: 3033-A 1qyi-A 15.0  3.5  198   375   19      0      0    17 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    hypothetical pro
12: 3033-A 2i6x-A 14.9  3.1  176   199   19      0      0    18 S    HYDROLASE        hydrolase, haloacid dehalogenase-like family 
13: 3033-A 1u7p-A 14.3  2.9  144   164   18      0      0    14 S    HYDROLASE        magnesium-dependent phosphatase-1 (mdp-1)       (
14: 3033-A 1ymq-A 14.1  2.3  130   260   16      0      0    14 S    TRANSFERASE      sugar-phosphate phosphatase bt4131      (bacte 
15: 3033-A 1j8d-A 13.1  2.5  141   180   11      0      0    12 S     HYDROLASE       deoxy-d-mannose-octulosonate 8-phosphate ph
16: 3033-A 2ho4-A 12.9  2.4  131   246   19      0      0    14 S    HYDROLASE        haloacid dehalogenase-like hydrolase domain 
17: 3033-A 1pw5-A 12.7  2.3  136   246   21      0      0    12 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    nagd protein, pu
18: 3033-A 1nf2-A 12.7  2.6  127   267   13      0      0    11 S    STRUCTURAL GENOMICS/UNKNOWN FUNCTION     phosphatase     (the 
19: 3033-A 1rlm-A 12.4  2.8  131   269   13      0      0    14 S    HYDROLASE        phosphatase Mutant      (escherichia coli) bacte
20: 3033-A 1f5s-A 12.1  3.5  159   210   14      0      0    15 S     HYDROLASE       phosphoserine phosphatase (psp)         (methanoco 
21: 3033-A 1cr6-B 12.0  3.8  177   541   18      0      0    18 S    HYDROLASE        epoxide hydrolase       (mus musculus) mouse expr
22: 3033-A 1rku-A 11.9  3.6  172   206   11      0      0    18 S    TRANSFERASE      homoserine kinase       (pseudomonas aeruginosa 
23: 3033-A 2b30-A 11.8  2.7  134   284   16      0      0    12 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    pvivax hypotheti
24: 3033-A 1kyt-A 10.5  2.5  122   216   13      0      0    15 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    hypothetical  pro 
25: 3033-A 2o2x-A 10.3  3.6  139   204   17      0      0    14 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    hypothetical pro
26: 3033-A 1u02-A 10.1  2.7  128   222   16      0      0    12 S    STRUCTURAL GENOMICS      trehalose-6-phosphate phosphatase 
27: 3033-A 2fea-A 10.0  3.5  167   219    7      0      0    21 S    HYDROLASE        2-hydroxy-3-keto-5-methylthiopentenyl-1- pho
28: 3033-A 2hx1-A  9.6  3.2  130   275   24      0      0    19 S    HYDROLASE        predicted sugar phosphatases of the had supe 
29: 3033-A 1mh9-A  9.2  3.2  146   194   15      0      0    15 S    HYDROLASE        deoxyribonucleotidase (mitochondrial  5'(3')-

Surface properties

From PDB

Chemical component identifier would be

PO4 PHOSPHATE ION

NA SODIUM ION

EDO 1,2-ETHANEDIOL

CL CHLORIDE ION

Closely related to 2HO4,PO4 PHOSPHATE ION found.

Cloesly related to 2HX1,CL Chloride Ion, EDO 1 2 Ethanediol found.

2GFH http://www.rcsb.org/pdb/explore/biologyAndChemistry.do?structureId=2GFH

2HX1 http://www.rcsb.org/pdb/explore/biologyAndChemistry.do?structureId=2HX1

1FEZ http://www.rcsb.org/pdb/explore/biologyAndChemistry.do?structureId=1FEZ

2HO4 http://www.rcsb.org/pdb/explore/biologyAndChemistry.do?structureId=2HO4

Pubmed

The identity of Asp12 as the active-site nucleophile was further evidenced by the observed removal of catalytic activity resulting from Asp12Ala substitution http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=10956028

Pfarm classification

PFAM Accession:PF00702

PFAM ID:hydrolase

http://www.sanger.ac.uk//cgi-bin/Pfam/getacc?PF00702

CE

2GFH USR1:A(size=260) vs 1FEZ USR2:A(size=256) Structure Alignment

2GFH USR1:A - MOL_ID: 1; MOLECULE: HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 4; CHAIN: A; ENGINEERED: YES

1FEZ USR2:A - MOL_ID: 1; MOLECULE: PHOSPHONOACETALDEHYDE HYDROLASE; CHAIN: A, B, C, D; ENGINEERED: YES

 USR1:A   17/6     RVRAVFFDLDNTLID-TAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHP
 USR2:A    1/6     KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRG--------VAITAEEARKPMGLL----
 USR1:A   76/#12   YSTCITDVRTSHWEEA--IQETKG---GADN--RKLAEECYFLWKST--RLQHMILADDV
 USR2:A   49/54    -----KIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINA
 USR1:A  127/116   KAMLTELRK--EVRLLLLTNGDRQTQREKIEACACQ-----SYFDAIVIGGEQKEEKPAP
 USR2:A  104/109   VKEVIASLRERGIKIGSTTG----YTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYP
 USR1:A  180/169   SIFYHCCDLLGVQP-GDCVMVGDTLETDIQGGLNAGLKATVWINK---------------
 USR2:A  160/165   WMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGM--WTVGVILGSSELGLTEEEVENM
 USR1:A  224/213   --------SGR-VPLTSSPMPHYMVSSVLELPALLQSI
 USR2:A  218/223   DSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHI

2gfh USR1:A - MOL_ID: 1; MOLECULE: HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 4; CHAIN: A; ENGINEERED: YES

2hx1 USR2:A - MOL_ID: 1; MOLECULE: PREDICTED SUGAR PHOSPHATASES OF THE HAD SUPERFAMILY; CHAIN: A, B, C, D; ENGINEERED: YES

 USR1:A   65/54    QVKLSKECFHPYST------------------------------CITDVRTSHWEEAIQE
 USR2:A   24/24    VLKTYNGL------LPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKL-------
 USR1:A   95/84    TKGGADNRKLAEECYFLWKSTRLQHM---ILADDVKAMLTELRKEVRLLLLTNGDRQTQR
 USR2:A   71/71    ----------GLFSI-TADKIISSGXITKEYIDLKVDGG-------IVAYLG------TA
 USR1:A  152/141   EKIEACACQSYFDAIV-----------------IGGEQKEEKPAPSIFYHCCDLLGVQPG
 USR2:A  107/107   NSANY-LVSDGIKXLPVSAIDDSNIGEVNALVLLDDEGF------NWFHDLNKTVNLLRK
 USR1:A  195/184   DC-VMVGDTL---------------ETDIQGGLNAGLKATVWI
 USR2:A  160/160   RTIPAIVANTDNTYPLTKTDVAIAIGGVATXIES-ILGRRFIR

2gfh USR1:A - MOL_ID: 1; MOLECULE: HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 4; CHAIN: A; ENGINEERED: YES

2ho4 USR2:A - MOL_ID: 1; MOLECULE: HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 2; CHAIN: A, B; ENGINEERED: YES

 USR1:A  122/111   LADDVKAMLTELRKEV--RLLLLTNGDRQTQREKIEACACQSYFD---------AIVIGG
 USR2:A   71/72    EIFTSLTAARNLIEQKQVRPXLLLD-----------DRALPEFTGVQTQDPNAVVIGLAP
 USR1:A  171/160   EQKEEKPAPSIFYHCCDLLGVQPGDCVMVGD-------------TLETDIQGGLNAGLKA
 USR2:A  120/121   EH----FHYQLLNQAFRLLLDG--APLIAIHKARYYKRKDGLALGPGPFVTALEYATDTK
 USR1:A  218/207   TVWINKSGRVPLTSSPMPHYMVSSVLELP
 USR2:A  174/175   AXV--------------------VGKPEK

2gfh vs 2hx1 Rmsd = 5.6Å Z-Score = 3.1 Sequence identity = 6.2% Aligned/gap positions = 112/111

2gfh vs 1fez Rmsd = 4.4Å Z-Score = 5.5 Sequence identity = 17.4% Aligned/gap positions = 213/65

2gfh vs 2ho4 Rmsd = 5.0Å Z-Score = 3.3 Sequence identity = 11.4% Aligned/gap positions = 88/61

ProFunc

http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bb32&code=143144

Diagram showing the conserved region ASN15 , Thr16, Leu17 with EDO4 molecule in grey and PO4 in yellow.

IMPORTANT!!! This is involved in the function. Most likely a phosphatase.

Most likely an antifreezer.

Possible binding sites. Results shows 2 ligands PO4 and EDO4

Pfam 21.0 (Janelia Farm)Alignments of top-scoring domains

Table of functions

Model Hydrolase

Seq-from:18

Seq-to:224

HMM-from:1

HMM-to:183

Score:96.2

E-value:1e-25

Alignment:glocal

Description:haloacid dehalogenase-like hydrolase Hydrolase: domain 1 of 1, from 18 to 224: score 96.2, E = 1e-25 *->ikavvFDkDGTLtdgkeppiaeaiveaaaelgl.........lplee ++av+FD+D+TL+d+ + + ++ + e+ ++l + + +++ ++ + query 18 VRAVFFDLDNTLIDT-AGASRRGMLEVIKLLQSkyhykeeaeIICDK 63 vekllgrgl.g.erilleggltaell...................d.evl v l +++ ++ ++ t ++ + +++++ ++++ ++ ++ query 64 VQVKLSKECfHpYSTCITDVRTSHWEeaiqetkggadnrklaeecYfLWK 113 glial.dklypgarealkaLkrrGikvailTggdr.naeallealgla.l ++ ++ l +++++ l +L++ +++ +lT+gdr++++++ ea+++ ++ query 114 STRLQhMILADDVKAMLTELRKE-VRLLLLTNGDRqTQREKIEACACQsY 162 fdviidsdevggvgpivvgKPkpeifllalerlgvkpeevgpevlmVGDg fd+i++++e + KP+p if + ++ lgv+p ++ +mVGD+ query 163 FDAIVIGGEQK------EEKPAPSIFYHCCDLLGVQPGDC----VMVGDT 202 vnDapalaa.AGv.gvamgngg<-* + +++ + +AG+++++++n + query 203 LETDIQGGLnAGLkATVWINKS 224

External Link

1. EBI Mcromolecular Structure Database

2. InterProScan

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