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PDBsum entry 4z9x
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Oxidoreductase
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PDB id
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4z9x
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Crystal structure of 2-keto-3-deoxy-d-gluconate dehydrogenase from streptococcus pyogenes
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Structure:
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Gluconate 5-dehydrogenase. Chain: a. Synonym: 2-keto-3-deoxy-d-gluconic acid 5-dehydrogenase, putative 5- keto-d-gluconate 5-reductase. Engineered: yes
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Source:
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Streptococcus pyogenes serotype m1. Organism_taxid: 301447. Gene: idno, m5005_spy0524, spy_0636. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Resolution:
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1.70Å
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R-factor:
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0.183
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R-free:
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0.201
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Authors:
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Y.Maruyama,R.Takase,S.Oiki,B.Mikami,K.Murata,W.Hashimoto
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Key ref:
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R.Takase
et al.
(2016).
Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity.
Proteins,
84,
934-947.
PubMed id:
DOI:
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Date:
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13-Apr-15
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Release date:
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29-Apr-15
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PROCHECK
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Headers
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References
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Q9A0T1
(Q9A0T1_STRP1) -
5-keto-D-gluconate 5-reductase from Streptococcus pyogenes serotype M1
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Seq:
Struc:
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264 a.a.
257 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Proteins
84:934-947
(2016)
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PubMed id:
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Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity.
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R.Takase,
Y.Maruyama,
S.Oiki,
B.Mikami,
K.Murata,
W.Hashimoto.
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ABSTRACT
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Short-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from
bacteria to humans, and has significant roles in metabolism of carbohydrates,
lipids, amino acids, and other biomolecules. An important intermediate in acidic
polysaccharide metabolism is 2-keto-3-deoxy-d-gluconate (KDG). Recently, two
short and long loops in Sphingomonas KDG-producing SDR enzymes (NADPH-dependent
A1-R and NADH-dependent A1-R') involved in alginate metabolism were shown to be
crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes-KduD from
Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes
(SpyDhuD)-prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH
and NADH. Both enzymes reduce 2,5-diketo-3-deoxy-d-gluconate to produce KDG.
Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with
NADH were determined at high resolution (approximately 1.6 Å) by X-ray
crystallography. Both PcaKduD and SpyDhuD consist of a three-layered structure,
α/β/α, with a coenzyme-binding site in the Rossmann fold; similar to enzymes
A1-R and A1-R', both arrange the two short and long loops close to the
coenzyme-binding site. The primary structures of the two loops in PcaKduD and
SpyDhuD were similar to those in A1-R' but not A1-R. Charge neutrality and
moderate space at the binding site of the nucleoside ribose 2' coenzyme region
were determined to be structurally crucial for dual-coenzyme specificity in
PcaKduD by structural comparison of the NADH- and NADPH-specific SDR enzymes.
The corresponding site in SpyDhuD was negatively charged and spatially shallow.
This is the first reported study on structural determinants in SDR family KduD
related to dual-coenzyme specificity. Proteins 2016; 84:934-947. © 2016 Wiley
Periodicals, Inc.
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