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3KBN
Biol. Unit 1
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Asym.Unit (147 KB)
Biol.Unit 1 (561 KB)
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Title
:
ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH 2NI(2+) CO-FACTORS AND D12-D-GLUCOSE IN THE LINEAR FORM
Authors
:
A. Y. Kovalevsky, L. Hanson, P. Langan
Date
:
20 Oct 09 (Deposition) - 16 Jun 10 (Release) - 07 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.53
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Xylose Isomerase, Linear D-Glucose, Carbohydrate Metabolism, Metal- Binding, Pentose Shunt, Xylose Metabolism, Isomerase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
A. Y. Kovalevsky, L. Hanson, S. Z. Fisher, M. Mustyakimov, S. A. Mason, V. T. Forsyth, M. P. Blakeley, D. A. Keen, T. Wagner, H. L. Carrell, A. K. Katz, J. P. Glusker, P. Langan
Metal Ion Roles And The Movement Of Hydrogen During Reactio Catalyzed By D-Xylose Isomerase: A Joint X-Ray And Neutron Diffraction Study.
Structure V. 18 688 2010
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: D-GLUCOSE IN LINEAR FORM (GLOa)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
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No.
Name
Count
Type
Full Name
1
GLO
4
Ligand/Ion
D-GLUCOSE IN LINEAR FORM
2
NI
-1
Ligand/Ion
NICKEL (II) ION
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Sites
(4, 4)
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:217 , HIS A:220 , ASP A:255 , NI A:392 , NI A:393 , GLO A:401 , HOH A:1001
BINDING SITE FOR RESIDUE NI A 391
2
AC2
SOFTWARE
GLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , NI A:391 , GLO A:401 , HOH A:1001
BINDING SITE FOR RESIDUE NI A 392
3
AC3
SOFTWARE
GLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , NI A:391 , GLO A:401
BINDING SITE FOR RESIDUE NI A 393
4
AC4
SOFTWARE
TRP A:16 , PHE A:26 , HIS A:54 , THR A:90 , VAL A:135 , TRP A:137 , GLU A:181 , LYS A:183 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:255 , ASP A:287 , NI A:391 , NI A:392 , NI A:393 , HOH A:1001 , HOH A:1096 , HOH A:1111
BINDING SITE FOR RESIDUE GLO A 401
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SAPs(SNPs)/Variants
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PROSITE Patterns/Profiles
(1, 4)
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1: XYLOSE_ISOMERASE (A:4-383)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
XYLOSE_ISOMERASE
PS51415
Xylose isomerase family profile.
XYLA_STRRU
4-383
4
A:4-383
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Exons
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SCOP Domains
(1, 1)
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1a: SCOP_d3kbna_ (A:)
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Xylose isomerase-like
(125)
Family
:
Xylose isomerase
(97)
Protein domain
:
D-xylose isomerase
(82)
Streptomyces rubiginosus [TaxId: 1929]
(31)
1a
d3kbna_
A:
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CATH Domains
(1, 1)
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all CATH domains
1a: CATH_3kbnA00 (A:1-388)
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Class
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Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Divalent-metal-dependent TIM barrel enzymes
(98)
Streptomyces rubiginosus. Organism_taxid: 1929.
(9)
1a
3kbnA00
A:1-388
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Pfam Domains
(1, 1)
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1a: PFAM_AP_endonuc_2_3kbnA01 (A:40-265)
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Clan
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TIM_barrel
(694)
Family
:
AP_endonuc_2
(72)
Streptomyces rubiginosus
(22)
1a
AP_endonuc_2-3kbnA01
A:40-265
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Asym.Unit (147 KB)
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