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ProFunc results for 4j9t

3D structure
Jmol   RasMol
Header details

Structure:
3 TARGET OR61

Source:
Micromonospora viridifaciens. Organism_taxid: 1881. Gene: neda. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Date:
17-Feb-13

Author(s):
F.Forouhar,S.Lew,J.Seetharaman,J.H.Mills,S.D.Khare,J.K.Evere D.Baker,G.T.Montelione,J.F.Hunt,L.Tong,Northeast Structural Consortium (Nesg)

Resolution:
1.40Å      

Waters:
527

Summary of predicted function

+ Protein name terms
sialidase (48.39) acid (10.55) neuraminidase (7.92) dana (6.12) trans-sialidase (4.40) active site (3.56) inhibitor (3.52) fragment (3.41)

+ Gene Ontology (GO) terms
Cellular component: cell (10.21) cell part (10.21) extracellular region (8.34) periplasmic space (2.36)
Biological process: metabolic process (73.16) carbohydrate metabolic process (13.11) primary metabolic process (13.11) pathogenesis (12.20)
Biochemical function: catalytic activity (92.98) hydrolase activity (88.08) hydrolase activity\, acting on glycosyl bonds (87.25) hydrolase activity\, hydrolyzing O\-glycosyl compounds (87.25)
The protein names and GO terms above are the most common terms found in the hits obtained from the analyses below. Each term's score (based on the number of times it occurs independently) is given in brackets. Click on the plus icons for a complete breakdown of which programs, and further, which hits the terms came from.

ProFunc results

Sequence motifs

InterPro scan for sequence motifs. Chain A

3 motifs matched in scan against PROSITE, PRINTS, PFam-A, TIGRFAM, PROFILES and PRODOM motifs

  Type Motif Name
1. Gene3D G3DSA:2.120.10.10
2. SUPERFAMILY SSF50939
3. PANTHER PTHR10628

Matches to the Superfamily HMM library

Search of sequence vs Superfamily HMM library. Chain A

No matching motifs were found in the sequence.

Matches to existing PDB structures

Sequence search vs existing PDB entries. Chain A

92 matching sequences found by FASTA search

  PDB code E-value %-tage id Overlap Name
1. 1eur(A) 2.6e-144 96.620 355 Sialidase
2. 1eus(A) 2.6e-144 96.620 355 Sialidase complexed with 2-deoxy-2,3-dehydro-n- acetylneuraminic acid
3. 1w8n(A) 3.2e-144 96.620 355 Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens.
4. 1w8o(A) 3.2e-144 96.620 355 Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens
5. 1eut(A) 4.4e-144 96.620 355 Sialidase, large 68kd form, complexed with galactose
... plus others

Sequence search

BLAST search vs Uniprot. Chain A

50 matching sequences found by BLAST search

  Ref. no. E-value %-tage id Overlap Name
1. NANH_MICVI 0.0 96.620 355 Q02834 Sialidase OS=Micromonospora viridifaciens GN=nedA PE=1
2. U2ABX1_9BACI 9e-166 72.034 354 U2ABX1 Uncharacterized protein (Fragment) OS=Bacillus sp. EGD-AK10
3. A0A0A0J426_9MICO 2e-165 71.831 355 A0A0A0J426 Uncharacterized protein OS=Knoellia sinensis KCTC
4. E7N6K2_9ACTO 2e-116 55.525 362 E7N6K2 BNR/Asp-box repeat protein (Fragment) OS=Actinomyces sp.
5. U1S1I8_9ACTO 3e-115 55.801 362 U1S1I8 BNR/Asp-box repeat protein OS=Actinomyces johnsonii F0542
... plus others

Residue conservation analysis

Conservation mapped onto 3D structure.

 

Gene neighbours

Neighbouring genes on genome. Chain A

No genome locations found for any homologues.

Matching folds detected by SSM

Matching folds. Chain A

1789 significant structural matches

  Q-score Rmsd No. SSE Z-score PDB Name
1. 0.934 0.48Å 25 24.5 1eus Sialidase complexed with 2-deoxy-2,3-dehydro-n- acetylneuraminic acid
2. 0.927 0.48Å 25 24.6 1eur Sialidase
3. 0.594 1.47Å 20 15.3 2f10 Crystal structure of the human sialidase neu2 in complex with peramivir inhibitor
4. 0.591 1.50Å 19 14.7 4ncs Human sialidase 2 in complex with 2,3-difluorosialic acid (c intermediate)
5. 0.591 1.56Å 20 14.9 2f0z Crystal structure of the human sialidase neu2 in complex with zanamivir inhibitor
... plus others

DNA-binding motifs (HTH)

Helix-turn-helix (HTH) motifs. Chain A

No HTH motifs were found in structure.

Nest analysis

Nest analysis. Chain A

11 nests located in the structure

  Score No.
resid.
Ave.
access-
ibility
Cleft Ave.
conser-
vation
Residues
1. 3.850 3 0.00 1 0.850 Asp378(A), Gly379(A), Thr380(A)
2. 2.742 5 0.00 2 0.742 Ala279(A), Arg280(A), Ser281(A), Gly282(A), Tyr283(A)
3. 1.786 3 0.00 5 0.786 Gly245(A), Arg246(A), Thr247(A)
4. 1.731 3 0.00 3 0.731 Gly354(A), Gln355(A), Thr356(A)
5. 0.932 3 0.00 - 0.932 Thr140(A), Gly141(A), Thr142(A)
... plus others

Cleft analysis

Surface clefts.

 

3D functional template searches

Enzyme active site templates.

No hits obtained from any of the 584 enzyme active site templates.

Ligand-binding templates.

4 significant hits out of 94055 ligand-binding templates.

  Score Template PDB Name
1. 119.688 PO4b0409 1mg3 Mutation of alpha phe55 of methylamine dehydrogenase alters the reorganization energy and electronic coupling for its electron transfer reaction with amicyanin
Het Group PO4
2. 116.406 NAGb0860 2ade Crystal structure of fructan 1-exohydrolase iia from cichori in complex with fructose
Het Group NAG
3. 114.500 DHEb0009 1aom Substrate and product bound to cytochrome cd1 nitrite reductase
Het Group DHE
4. 101.445 DHEb0017 1bl9 Conformational changes occurring upon reduction in nitrite reductase from pseudomonas aeruginosa
Het Group DHE

DNA-binding templates.

No hits obtained from any of the 5320 DNA-binding templates.

Reverse template comparison vs structures in PDB.

20 significant hits out of 400 auto-generated templates.

  Score Template PDB Name
1. 1080.000 TMP00278 4j9t Crystal structure of a putative, de novo designed unnatural dependent metalloprotein, northeast structural genomics con target or61
2. 1019.688 TMP00182 1w8o Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens
3. 1009.375 TMP00278 1eur Sialidase
4. 568.938 TMP00065 4q6k Crystal structure of a putative neuraminidase (baccac_01090) bacteroides caccae atcc 43185 at 1.90 a resolution (psi com target)
5. 568.938 TMP00065 4bbw The crystal structure of sialidase vpi 5482 (btsa) from bacteroides thetaiotaomicron
... plus others

Key

In the summaries above, the hits are coloured according to their likelihood of being correct as follows: certain matches, probable matches, possible matches, and long shots. If the reliability of a hit is unknown, it is shown in navy blue.

Generated on Thu 26 Feb 2015 spacer

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