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1XYM
Biol. Unit 1
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Asym.Unit (179 KB)
Biol.Unit 1 (341 KB)
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(1)
Title
:
THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID
Authors
:
K. N. Allen, A. Lavie, G. A. Petsko, D. Ringe
Date
:
07 Dec 93 (Deposition) - 31 May 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Isomerase(Intramolecular Oxidoreductase)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. N. Allen, A. Lavie, A. Glasfeld, T. N. Tanada, D. P. Gerrity, S. C. Carlson, G. K. Farber, G. A. Petsko, D. Ringe
Role Of The Divalent Metal Ion In Sugar Binding, Ring Opening, And Isomerization By D-Xylose Isomerase: Replacement Of A Catalytic Metal By An Amino Acid.
Biochemistry V. 33 1488 1994
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: D-GLUCOSE IN LINEAR FORM (GLOa)
1b: D-GLUCOSE IN LINEAR FORM (GLOb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: HYDROXIDE ION (OHa)
3b: HYDROXIDE ION (OHb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GLO
4
Ligand/Ion
D-GLUCOSE IN LINEAR FORM
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
OH
-1
Ligand/Ion
HYDROXIDE ION
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: M1A (AUTHOR)
08: M1B (AUTHOR)
09: M2A (AUTHOR)
10: M2B (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:53 , THR A:89 , PHE A:93 , VAL A:134 , TRP A:136 , LYS A:180 , LYS A:182 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:286 , HOH A:1263 , HOH A:1268 , OH A:1700 , PHE B:525
BINDING SITE FOR RESIDUE GLO A 950
02
AC2
SOFTWARE
PHE A:25 , HIS B:553 , THR B:589 , PHE B:593 , VAL B:634 , TRP B:636 , LYS B:680 , LYS B:682 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:786 , MG B:901 , HOH B:1345 , OH B:1800
BINDING SITE FOR RESIDUE GLO B 960
03
AC3
SOFTWARE
GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , OH A:1700
BINDING SITE FOR RESIDUE MG A 401
04
AC4
SOFTWARE
GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , MG A:401 , GLO A:950
BINDING SITE FOR RESIDUE OH A 1700
05
AC5
SOFTWARE
GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , GLO B:960 , OH B:1800
BINDING SITE FOR RESIDUE MG B 901
06
AC6
SOFTWARE
GLU B:716 , ASP B:754 , ASP B:756 , MG B:901 , GLO B:960
BINDING SITE FOR RESIDUE OH B 1800
07
M1A
AUTHOR
LYS A:180 , ASP A:244 , ASP A:286 , GLU A:216 , GLO A:950
WHILE THE ACTIVE SITE IN THE WILD TYPE ENZYME CONTAINS THE METAL BINDING SITE, IN THIS MUTANT THE METAL IONS IN THESE SITES ARE REPLACED BY THE N-EPSILON AMINO GROUPS OF LYS
08
M1B
AUTHOR
LYS B:680 , ASP B:744 , ASP B:786 , GLU B:716 , GLO B:960
WHILE THE ACTIVE SITE IN THE WILD TYPE ENZYME CONTAINS THE METAL BINDING SITE, IN THIS MUTANT THE METAL IONS IN THESE SITES ARE REPLACED BY THE N-EPSILON AMINO GROUPS OF LYS
09
M2A
AUTHOR
MG A:401 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , OH A:1700
METAL BINDING SITE
10
M2B
AUTHOR
MG B:901 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , OH B:1800
METAL BINDING SITE
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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, 4)
Info
All PROSITE Patterns/Profiles
1: XYLOSE_ISOMERASE (A:3-382,B:503-882)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
XYLOSE_ISOMERASE
PS51415
Xylose isomerase family profile.
XYLA_STROL
4-383
4
A:3-382
B:503-882
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Exons
(0, 0)
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1xyma_ (A:)
1b: SCOP_d1xymb_ (B:)
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)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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 olivochromogenes [TaxId: 1963]
(9)
1a
d1xyma_
A:
1b
d1xymb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1xymA00 (A:1-386)
1b: CATH_1xymB00 (B:501-886)
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)
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)
Organisms
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)
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Divalent-metal-dependent TIM barrel enzymes
(98)
Streptomyces olivochromogenes. Organism_taxid: 1963
(6)
1a
1xymA00
A:1-386
1b
1xymB00
B:501-886
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_AP_endonuc_2_1xymB01 (B:539-764)
1b: PFAM_AP_endonuc_2_1xymB02 (B:539-764)
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)
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)
Clan
:
TIM_barrel
(694)
Family
:
AP_endonuc_2
(72)
Streptomyces olivochromogenes
(8)
1a
AP_endonuc_2-1xymB01
B:539-764
1b
AP_endonuc_2-1xymB02
B:539-764
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Show PDB file:
Asym.Unit (179 KB)
Header - Asym.Unit
Biol.Unit 1 (341 KB)
Header - Biol.Unit 1
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