SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_010876999.1 NCBI__GCF_000008645.1:WP_010876999.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 11 hits to proteins with known functional sites (download)

Q58667 Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
54% identity, 97% coverage: 1:157/162 of query aligns to 3:159/170 of Q58667

query
sites
Q58667

M

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R26 (≠ V24) mutation R->K,V: Allows the recognition of substrates of IPMI enzymes since it becomes able to efficiently catalyze citraconate hydration and 3-isopropylmalate dehydration. Largely decreases substrate affinity for cis-homo(1-3)-aconitate.
T27 (≠ M25) mutation to A: Largely decreases substrate affinity for cis-homo(1-3)-aconitate while slightly increases activity on these substrates, and also decreases substrate affinity for maleate. Gains the ability to hydrate citraconate, an IPMI substrate.

2pkpA Crystal structure of 3-isopropylmalate dehydratase (leud)from methhanocaldococcus jannaschii dsm2661 (mj1271) (see paper)
54% identity, 97% coverage: 1:157/162 of query aligns to 3:159/167 of 2pkpA

query
sites
2pkpA

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binding zinc ion: D13 (= D11), C63 (= C61)

O14289 3-isopropylmalate dehydratase; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
35% identity, 79% coverage: 11:138/162 of query aligns to 554:697/758 of O14289

query
sites
O14289

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Sites not aligning to the query:

486 modified: Phosphoserine
488 modified: Phosphoserine

P9WK95 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
36% identity, 77% coverage: 11:135/162 of query aligns to 18:154/198 of P9WK95

query
sites
P9WK95

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K154 (= K135) modified: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)

P09339 Aconitate hydratase A; ACN; Aconitase; Aconitate/2-methylaconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.- from Bacillus subtilis (strain 168) (see 2 papers)
42% identity, 48% coverage: 48:124/162 of query aligns to 777:857/909 of P09339

query
sites
P09339

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Sites not aligning to the query:

1 modified: Initiator methionine, Removed
450 C→S: Loss of aconitase activity. It is glutamate auxotroph and accumulates citrate. Exhibits overexpression of the citB promoter and accumulates high levels of inactive aconitase.
741 R→E: Same aconitase activity compared to the wild-type. It is glutamate prototroph and accumulates citrate. Exhibits overexpression of the citB promoter and accumulates high levels of active aconitase.

3snpA Crystal structure analysis of iron regulatory protein 1 in complex with ferritin h ire RNA (see paper)
31% identity, 65% coverage: 53:157/162 of query aligns to 729:847/850 of 3snpA

query
sites
3snpA

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active site: S739 (= S63), R741 (= R65)
binding : R741 (= R65)

Sites not aligning to the query:

active site: 124, 125, 186, 505
binding : 125, 126, 188, 243, 250, 279, 283, 352, 357, 360, 419, 420, 421, 504, 505, 520, 642, 643, 644, 645, 646, 649, 665, 669, 671, 674

P21399 Cytoplasmic aconitate hydratase; Aconitase; Citrate hydro-lyase; Ferritin repressor protein; Iron regulatory protein 1; IRP1; Iron-responsive element-binding protein 1; IRE-BP 1; EC 4.2.1.3 from Homo sapiens (Human) (see 2 papers)
31% identity, 65% coverage: 53:157/162 of query aligns to 768:886/889 of P21399

query
sites
P21399

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S778 (= S63) mutation to A: No effect on iron-regulated RNA binding. Loss of aconitase activity.
R780 (= R65) mutation to Q: Nearly abolishes RNA binding.

Sites not aligning to the query:

300 C→S: No effect on aconitase activity or on RNA binding.
318 T → M: in dbSNP:rs150373174
437 C→S: Loss of aconitase activity. Leads to constitutive RNA binding, irrespective of iron levels.
503 C→S: Loss of aconitase activity. Leads to constitutive RNA binding, irrespective of iron levels.
506 C→S: Loss of aconitase activity. Leads to constitutive RNA binding, irrespective of iron levels.
536 R→Q: Strongly reduced RNA binding.
541 R→Q: Strongly reduced RNA binding.
699 R→K: No effect on RNA binding.

2b3xA Structure of an orthorhombic crystal form of human cytosolic aconitase (irp1) (see paper)
31% identity, 65% coverage: 53:157/162 of query aligns to 767:885/888 of 2b3xA

query
sites
2b3xA

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active site: S777 (= S63), R779 (= R65)

Sites not aligning to the query:

active site: 124, 125, 204, 535
binding iron/sulfur cluster: 175, 206, 436, 502, 505, 506, 534

P19414 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
41% identity, 41% coverage: 53:118/162 of query aligns to 656:723/778 of P19414

query
sites
P19414

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I

K

N

K

V

Q

G

G

-

L

I

L

P

P

L

L

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N

L

F

E

K

A

N

P

P

G

A

I

D

T

Y

E

D

K

K

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N

N

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G

D

D

D

E

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I

E

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I

Sites not aligning to the query:

1:16 modified: transit peptide, Mitochondrion
604 R→K: Strongly diminishes the catalytic activity towards both known substrates, aconitate and homoaconitate.

D9X0I3 Aconitate hydratase A; ACN; Aconitase; EC 4.2.1.3 from Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494) (see paper)
44% identity, 32% coverage: 53:104/162 of query aligns to 806:857/931 of D9X0I3

query
sites
D9X0I3

I

V

V

L

A

A

G

G

K

K

N

E

F

Y

G

G

C

S

G

G

S

S

R

R

E

D

H

W

A

A

P

A

L

K

A

G

L

T

K

A

G

L

A

L

G

G

I

V

A

K

A

A

V

V

I

I

A

A

E

E

S

S

F

Y

A

E

R

R

I

I

F

H

Y

R

R

S

N

N

A

L

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I

N

G

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M

G

G

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L

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L

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A

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P

Sites not aligning to the query:

125:129 mutation Missing: Retains 40% of aconitase activity. Improves RNA-binding ability.
538 C→A: Loss of aconitase activity. Cannot rescue the growth defect of a disruption mutant and results in only a slight increase in PTT production in the mutant. Shows weak IRE-binding activity.
763 R→E: Loss of aconitase activity and IRE-binding activity; when associated with E-767.
767 Q→E: Loss of aconitase activity and IRE-binding activity; when associated with E-763.

A0QX20 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
30% identity, 56% coverage: 15:105/162 of query aligns to 758:864/943 of A0QX20

query
sites
A0QX20

D

E

I

V

I

M

I

I

P

R

G

G

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N

M

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K

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K

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G

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D

A

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F

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I

-

Y

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D

-

A

-

S

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-

N

-

Y

-

K

-

A

-

G

-

I

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P

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-

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V

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G

G

G

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K

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E

F

Y

G

G

C

S

G

G

S

S

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R

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A

A

P

A

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K

A

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L

T

K

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G

L

A

L

G

G

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K

A

A

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V

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I

A

T

E

E

S

S

F

F

A

E

R

R

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I

F

H

Y

R

R

S

N

N

A

L

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I

N

G

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M

G

G

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V

P

I

L

P

L

L

E

Q

A

F

P

P

G

A

Sites not aligning to the query:

394 modified: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)

Query Sequence

>WP_010876999.1 NCBI__GCF_000008645.1:WP_010876999.1
MKGKVWKFPDDVDTDIIIPGRYLVMRDPEKLREHVMEGLDPEFPSKVKPGDFIVAGKNFG
CGSSREHAPLALKGAGIAAVIAESFARIFYRNAINVGIPLLEAPGITEKLNEGDEIEVDL
DRGVIIRGDDEFPFKKLPDFMVEILEKGGLIPYLKKKGDFKG

Or try a new SitesBLAST search

SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory