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1YCH
Biol. Unit 1
Info
Asym.Unit (271 KB)
Biol.Unit 1 (134 KB)
Biol.Unit 2 (135 KB)
Biol.Unit 3 (262 KB)
Biol.Unit 4 (134 KB)
Biol.Unit 5 (135 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURES OF MOORELLA THERMOACETICA FPRA. NOVEL DIIRON SITE STRUCTURE AND MECHANISTIC INSIGHTS INTO A SCAVENGING NITRIC OXIDE REDUCTASE
Authors
:
R. Silaghi-Dumitrescu, D. M. Kurtz, W. N. Lanzilotta
Date
:
22 Dec 04 (Deposition) - 19 Apr 05 (Release) - 21 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: B,D (1x)
Biol. Unit 5: A,C (1x)
Keywords
:
Nitric Oxide, Reductase, Diiron Site, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
R. Silaghi-Dumitrescu, D. M. Kurtz Jr, L. G. Ljungdahl, W. N. Lanzilotta
X-Ray Crystal Structures Of Moorella Thermoacetica Fpra. Novel Diiron Site Structure And Mechanistic Insights Into A Scavenging Nitric Oxide Reductase.
Biochemistry V. 44 6492 2005
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: MU-OXO-DIIRON (FEOa)
1b: MU-OXO-DIIRON (FEOb)
1c: MU-OXO-DIIRON (FEOc)
1d: MU-OXO-DIIRON (FEOd)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FEO
2
Ligand/Ion
MU-OXO-DIIRON
2
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:2 , GLU A:60 , HIS C:271 , ASP C:275 , ZN C:621
BINDING SITE FOR RESIDUE ZN A 600
02
AC2
SOFTWARE
HIS A:271 , ASP A:275 , SER C:2 , GLU C:60 , ZN C:620
BINDING SITE FOR RESIDUE ZN A 601
03
AC3
SOFTWARE
SER B:2 , GLU B:60 , HIS D:271 , ASP D:275 , ZN D:631
BINDING SITE FOR RESIDUE ZN B 610
04
AC4
SOFTWARE
HIS B:271 , ASP B:275 , SER D:2 , GLU D:60 , ZN D:630
BINDING SITE FOR RESIDUE ZN B 611
05
AC5
SOFTWARE
HIS A:271 , ASP A:275 , ZN A:601 , SER C:2 , GLU C:60
BINDING SITE FOR RESIDUE ZN C 620
06
AC6
SOFTWARE
SER A:2 , GLU A:60 , ZN A:600 , HIS C:271 , ASP C:275
BINDING SITE FOR RESIDUE ZN C 621
07
AC7
SOFTWARE
HIS B:271 , ASP B:275 , ZN B:611 , SER D:2 , GLU D:60
BINDING SITE FOR RESIDUE ZN D 630
08
AC8
SOFTWARE
SER B:2 , GLU B:60 , ZN B:610 , HIS D:271 , ASP D:275
BINDING SITE FOR RESIDUE ZN D 631
09
AC9
SOFTWARE
HIS A:81 , GLU A:83 , ASP A:85 , HIS A:86 , HIS A:148 , ASP A:167 , HIS A:228 , HOH A:705
BINDING SITE FOR RESIDUE FEO A 501
10
BC1
SOFTWARE
THR A:261 , MET A:262 , TRP A:263 , LEU A:264 , SER A:265 , THR A:266 , PRO A:312 , THR A:313 , ILE A:314 , ASN A:315 , ASN A:316 , TYR A:345 , GLY A:346 , TRP A:347 , GLY A:348 , GLY A:349 , TRP A:376 , HIS B:25 , GLU B:83 , HIS B:148 , TRP B:149
BINDING SITE FOR RESIDUE FMN A 701
11
BC2
SOFTWARE
HIS B:81 , GLU B:83 , ASP B:85 , HIS B:86 , HIS B:148 , ASP B:167 , HIS B:228 , HOH B:714
BINDING SITE FOR RESIDUE FEO B 511
12
BC3
SOFTWARE
GLU A:83 , HIS A:148 , TRP A:149 , HOH A:706 , THR B:261 , MET B:262 , TRP B:263 , LEU B:264 , SER B:265 , THR B:266 , PRO B:312 , THR B:313 , ILE B:314 , ASN B:315 , ASN B:316 , ALA B:344 , TYR B:345 , GLY B:346 , TRP B:347 , GLY B:348 , GLY B:349 , TRP B:376 , HOH B:725 , HOH B:728 , HOH B:748
BINDING SITE FOR RESIDUE FMN B 711
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: FLAVODOXIN_LIKE (A:255-394,B:255-394)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FLAVODOXIN_LIKE
PS50902
Flavodoxin-like domain profile.
FPRA_MOOTA
255-394
2
A:255-394
B:255-394
-
-
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ycha2 (A:2-250)
1b: SCOP_d1ychb2 (B:2-250)
1c: SCOP_d1ychc2 (C:2-250)
1d: SCOP_d1ychd2 (D:2-250)
2a: SCOP_d1ycha1 (A:251-399)
2b: SCOP_d1ychb1 (B:251-399)
2c: SCOP_d1ychc1 (C:251-399)
2d: SCOP_d1ychd1 (D:251-399)
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Protein Domains
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-hydrolase/oxidoreductase
(184)
Superfamily
:
Metallo-hydrolase/oxidoreductase
(184)
Family
:
ROO N-terminal domain-like
(9)
Protein domain
:
Nitric oxide reductase N-terminal domain
(4)
Moorella thermoacetica [TaxId: 1525]
(3)
1a
d1ycha2
A:2-250
1b
d1ychb2
B:2-250
1c
d1ychc2
C:2-250
1d
d1ychd2
D:2-250
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Flavoproteins
(208)
Family
:
Flavodoxin-related
(81)
Protein domain
:
Nitric oxide reductase C-terminal domain
(4)
Moorella thermoacetica [TaxId: 1525]
(3)
2a
d1ycha1
A:251-399
2b
d1ychb1
B:251-399
2c
d1ychc1
C:251-399
2d
d1ychd1
D:251-399
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ychA02 (A:254-396)
1b: CATH_1ychB02 (B:254-396)
1c: CATH_1ychC02 (C:254-396)
1d: CATH_1ychD02 (D:254-396)
2a: CATH_1ychA01 (A:2-248)
2b: CATH_1ychB01 (B:2-248)
2c: CATH_1ychC01 (C:2-248)
2d: CATH_1ychD01 (D:2-248)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.360, no name defined]
(150)
Moorella thermoacetica. Organism_taxid: 1525.
(1)
1a
1ychA02
A:254-396
1b
1ychB02
B:254-396
1c
1ychC02
C:254-396
1d
1ychD02
D:254-396
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Metallo-beta-lactamase; Chain A
(92)
Homologous Superfamily
:
Metallo-beta-lactamase, chain A
(92)
Moorella thermoacetica. Organism_taxid: 1525.
(1)
2a
1ychA01
A:2-248
2b
1ychB01
B:2-248
2c
1ychC01
C:2-248
2d
1ychD01
D:2-248
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Flavodoxin_1_1ychD01 (D:257-390)
1b: PFAM_Flavodoxin_1_1ychD02 (D:257-390)
1c: PFAM_Flavodoxin_1_1ychD03 (D:257-390)
1d: PFAM_Flavodoxin_1_1ychD04 (D:257-390)
2a: PFAM_Lactamase_B_1ychD05 (D:32-241)
2b: PFAM_Lactamase_B_1ychD06 (D:32-241)
2c: PFAM_Lactamase_B_1ychD07 (D:32-241)
2d: PFAM_Lactamase_B_1ychD08 (D:32-241)
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(
)
(
)
Clan
:
Flavoprotein
(71)
Family
:
Flavodoxin_1
(23)
Moorella thermoacetica (strain ATCC 39073)
(2)
1a
Flavodoxin_1-1ychD01
D:257-390
1b
Flavodoxin_1-1ychD02
D:257-390
1c
Flavodoxin_1-1ychD03
D:257-390
1d
Flavodoxin_1-1ychD04
D:257-390
Clan
:
Metallo-HOrase
(67)
Family
:
Lactamase_B
(53)
Moorella thermoacetica (strain ATCC 39073)
(2)
2a
Lactamase_B-1ychD05
D:32-241
2b
Lactamase_B-1ychD06
D:32-241
2c
Lactamase_B-1ychD07
D:32-241
2d
Lactamase_B-1ychD08
D:32-241
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