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T0547

© 2010 Grishin lab/HHMI/UTSW

updated on 2010-12-20

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643

T0547

BR53 from unknown species

Target sequence:

>T0547 BR53, unknown species, 611 residues
MMDYGIDIWGNENFIIKNGKVCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVGIWAKSGGINSKFGLTSTELIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPSNALEYLHDSIDHLESILTLFDLGYVDLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGLEQNFPIMPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGMKHNLFTHPTEAIISINEKGYEVEGIIEAQSILDTLEDLDYDIHAIMDILNERISNSKLVNDKQKKHILGELYLFLNDNGYLKSIGV

HHsearch_pdb70_15May10,  HHsearch_scop70_1.75,  HHsearch_pfamA.24.0, HorAServer,  HorAServer (T0547d1),  HorAServer (T0547d2),  HorAServer (T0547d3),  HorAServer (T0547d4),  Dali Result

Structure:

Method: X-ray, res= Å, R/Rfree=

Determined by: NESG

PDB ID: 3nzp

Domains:   PyMOL of domains

Four domains.

To compute the weighted sum, GDT-TS for each domain was multiplied by the domain length, and this sum was divided by the sum of domain lengths. Each point represents first server model. Green, gray and black points are top 10, bottom 25% and the rest of prediction models. Blue line is the best-fit slope line (intersection 0) to the top 10 server models. Red line is the diagonal. Slope and root mean square y-x distance for the top 10 models (average difference between the weighted sum of domain GDT-TS scores and the whole chain GDT-TS score) are shown above the plot.

Structure classification:

The description below was written months before target structure release, thus it only presents shuoyong's personal thoughts simply based on sequence. Please be aware that it may contain laughable errors. It is certainly not our final assessment on this target. We will revise this section (and the sequence classification too) in a short time

This looks like a homologue of T0515. It contains at least two domains. N-termina (around 57-328) is Tim-barrel PLP-binding barrel, Alanine racemase-like, N-terminal domain; C-terminal ((around 322-538) is a C-terminal sheet domain: Eukaryotic ODC-like with greek key motif, Diaminopimelate decarboxylase LysA C-terminal like. The rest part of this protein is not clear to me.

CASP category:

T0547 needs domain-based evaluation

1st domain: TBM  alignment. 2nd domain: TBM  alignment. 3rd domain: FM  alignment. 4th domain: FM  alignment.

Closest templates:

Template manually selected by shuoyong:

1twi_A | PyMOL of 1twi A, alignment between target and this template covers 8-562 of target sequence.

  

Template selected by HHpred server group:

• 2o0t_A | PyMOL

• 7odc_A | PyMOL | this pdbchain contains scop domain: d7odca1 A:2-43,A:284-418, d7odca2 A:44-283

• 1twi_A | PyMOL | this pdbchain contains scop domain: d1twia1 A:15-49,A:314-448, d1twia2 A:50-313

Target sequence - PDB file inconsistencies:

Sequence classification:

N-terminal: Orn_Arg_deC_N, Pyridoxal-dependent decarboxylase, pyridoxal binding domain (PF02784); C-terminal: Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain (PF00278).

All predictions:

TS (GDT_TS score), TR (GDT_TS with penalty [reference]

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