1BWZ | pdb_00001bwz

DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE

• PDB DOI: https://doi.org/10.2210/pdb1BWZ/pdb

• Classification: ISOMERASE
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-09-29 Released: 1998-12-16 
• Deposition Author(s): Cirilli, M., Zheng, R., Scapin, G., Blanchard, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.242 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.

Cirilli, M., Zheng, R., Scapin, G., Blanchard, J.S.

(1998) Biochemistry 37: 16452-16458

• PubMed: 9843410 
• DOI: https://doi.org/10.1021/bi982138o
• Primary Citation Related Structures: 
  1BWZ


• PubMed Abstract: 
  

  The Haemophilus influenzae diaminopimelate epimerase was cloned, expressed, purified, and crystallized in the C2221 space group (a = 102.1 A, b = 115.4 A, c = 66.3 A, alpha = beta = gamma = 90 degrees). The three-dimensional structure was solved to 2.7 A using a single Pt derivative and the Se-Met-substituted enzyme to a conventional R factor of 19.0% (Rfree = 24.2%). The 274 amino acid enzyme consists of two structurally homologous domains, each containing eight beta-strands and two alpha-helices. Diaminopimelate epimerase is a representative of the PLP-independent amino acid racemases, for which no structure has yet been determined and substantial evidence exists supporting the role of two cysteine residues as the catalytic acid and base. Cys73 of the amino terminal domain is found in disulfide linkage, at the domain interface, with Cys217 of the carboxy terminal domain, and we suggest that these two cysteine residues in the reduced, active enzyme function as the acid and base in the mechanism.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.3 kDa 
• Atom Count: 2,146 
• Modeled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DIAMINOPIMELATE EPIMERASE)	A	274	Haemophilus influenzae	Mutation(s): 0  Gene Names: DAPF EC: 5.1.1.7
UniProt
Find proteins for P44859 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44859  Go to UniProtKB:  P44859

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.242 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.1	α = 90
b = 115.4	β = 90
c = 66.3	γ = 90

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-16 
Deposition Author(s): Cirilli, M., Zheng, R., Scapin, G., Blanchard, J.S.

Revision History  

• Version 1.0: 1998-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary