1BVR | pdb_00001bvr

M.TB. ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH NAD+ AND C16-FATTY-ACYL-SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.344 (Depositor), 0.342 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate.

Rozwarski, D.A.Vilcheze, C.Sugantino, M.Bittman, R.Sacchettini, J.C.

(1999) J Biological Chem 274: 15582-15589

  • DOI: https://doi.org/10.1074/jbc.274.22.15582
  • Primary Citation Related Structures: 
    1BVR

  • PubMed Abstract: 

    Enoyl-ACP reductases participate in fatty acid biosynthesis by utilizing NADH to reduce the trans double bond between positions C2 and C3 of a fatty acyl chain linked to the acyl carrier protein. The enoyl-ACP reductase from Mycobacterium tuberculosis, known as InhA, is a member of an unusual FAS-II system that prefers longer chain fatty acyl substrates for the purpose of synthesizing mycolic acids, a major component of mycobacterial cell walls. The crystal structure of InhA in complex with NAD+ and a C16 fatty acyl substrate, trans-2-hexadecenoyl-(N-acetylcysteamine)-thioester, reveals that the substrate binds in a general "U-shaped" conformation, with the trans double bond positioned directly adjacent to the nicotinamide ring of NAD+. The side chain of Tyr158 directly interacts with the thioester carbonyl oxygen of the C16 fatty acyl substrate and therefore could help stabilize the enolate intermediate, proposed to form during substrate catalysis. Hydrophobic residues, primarily from the substrate binding loop (residues 196-219), engulf the fatty acyl chain portion of the substrate. The substrate binding loop of InhA is longer than that of other enoyl-ACP reductases and creates a deeper substrate binding crevice, consistent with the ability of InhA to recognize longer chain fatty acyl substrates.


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

Macromolecule Content 

  • Total Structure Weight: 175.95 kDa 
  • Atom Count: 12,987 
  • Modeled Residue Count: 1,608 
  • Deposited Residue Count: 1,608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
A, B, C, D, E
A, B, C, D, E, F
268Mycobacterium tuberculosisMutation(s): 0 
EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
M [auth D]
N [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
N [auth E],
O [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
THT

Query on THT



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth C],
P [auth F]
TRANS-2-HEXADECENOYL-(N-ACETYL-CYSTEAMINE)-THIOESTER
C20 H39 N O2 S
GDVZALUOXPTSHD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.344 (Depositor), 0.342 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.08α = 90
b = 83.45β = 95.24
c = 192.81γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-17
    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: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-03-10
    Changes: Derived calculations
  • Version 1.5: 2023-08-09
    Changes: Data collection, Database references, Refinement description