PDBsum entry 1e5k

Molybdopterin nucleotidyl-transferase

PDB id: 1e5k

Contents

Protein chain

188 a.a. *

Ligands

CIT ×2

Metals

_LI

Waters ×149

* Residue conservation analysis

PDB id:

1e5k

Name:

Molybdopterin nucleotidyl-transferase

Title:

Crystal structure of the molybdenum cofactor biosynthesis protein moba (protein fa) from escherichia coli at near atomic resolution

Structure:

Molybdopterin-guanine dinucleotide biosynthesis protein a. Chain: a. Synonym: moba, protein fa. Engineered: yes. Other_details: the wild-type construct was c-terminally extended with a 7-residue nickel affinity tag of sequence ser-his-his-his-his-his- his.

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Cellular_location: cytoplasm. Gene: moba. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: m15[prep4].

Resolution:

1.35Å R-factor: 0.184 R-free: 0.213

Authors:

C.E.M.Stevenson,F.Sargent,G.Buchanan,T.Palmer,D.M.Lawson

Key ref:

C.E.Stevenson et al. (2000). Crystal structure of the molybdenum cofactor biosynthesis protein MobA from Escherichia coli at near-atomic resolution. Structure, 8, 1115-1125. PubMed id: 11080634 DOI: 10.1016/S0969-2126(00)00518-9

Date:

27-Jul-00 Release date: 07-Nov-00

Protein chain

P32173  (MOBA_ECOLI) -  Molybdenum cofactor guanylyltransferase from Escherichia coli (strain K12)

Seq: 194 a.a.

Struc: 188 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.77 - molybdenum cofactor guanylyltransferase.
• Reaction: Mo-molybdopterin + GTP + H⁺ = Mo-molybdopterin guanine dinucleotide + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S0969-2126(00)00518-9

Structure 8:1115-1125 (2000)

PubMed id: 11080634

Crystal structure of the molybdenum cofactor biosynthesis protein MobA from Escherichia coli at near-atomic resolution.

C.E.Stevenson, F.Sargent, G.Buchanan, T.Palmer, D.M.Lawson.

ABSTRACT

BACKGROUND: All mononuclear molybdoenzymes bind molybdenum in a complex with an organic cofactor termed molybdopterin (MPT). In many bacteria, including Escherichia coli, molybdopterin can be further modified by attachment of a GMP group to the terminal phosphate of molybdopterin to form molybdopterin guanine dinucleotide (MGD). This modification reaction is required for the functioning of many bacterial molybdoenzymes, including the nitrate reductases, dimethylsulfoxide (DMSO) and trimethylamine-N-oxide (TMAO) reductases, and formate dehydrogenases. The GMP attachment step is catalyzed by the cellular enzyme MobA. RESULTS: The crystal structure of the 21.6 kDa E. coli MobA has been determined by MAD phasing with selenomethionine-substituted protein and subsequently refined at 1. 35 A resolution against native data. The structure consists of a central, predominantly parallel beta sheet sandwiched between two layers of alpha helices and resembles the dinucleotide binding Rossmann fold. One face of the molecule bears a wide depression that is lined by a number of strictly conserved residues, and this feature suggests that this is where substrate binding and catalysis take place. CONCLUSIONS: Through comparisons with a number of structural homologs, we have assigned plausible functions to several of the residues that line the substrate binding pocket. The enzymatic mechanism probably proceeds via a nucleophilic attack by MPT on the GMP donor, most likely GTP, to produce MGD and pyrophosphate. By analogy with related enzymes, this process is likely to require magnesium ions.

Selected figure(s)

Figure 5.
Figure 5. The Putative Substrate Binding Pocket of MobA(a) Ribbon diagram showing the locations of strictly conserved surface residues. The diagram was produced with MOLSCRIPT [53] and Raster3D [54] (blue = nitrogen, RED = oxygen, YELLOW = carbon).(b) Molecular surface displaying degrees of sequence identity for residues in and around the pocket according to the alignment shown in Figure 4. Warm colors indicate a high level of sequence identity, while cold colors indicate little or no conservation. Strictly conserved residues are shown in red.(b) Electrostatic surface potentials of MobA. Potentials of less than -10 kT, neutral, and greater than 10 kT are displayed in red, white, and blue, respectively.Surfaces for (a) and (b) were calculated with SwissPDBviewer [55] (http://www.expasy.ch/spdbv) and rendered using POV-Ray (http://www.povray.org). In order to get a more accurate impression of the surface conservations and charge, those side chains that could not be confidently placed in electron density were inserted and modeled into energetically favorable conformations. This was necessary for only one strictly conserved residue, namely Arg-19. All parts of this figure display the same view of the molecule. The white line delineates the proposed substrate binding pocket, and the labels A-D are for use in the discussion

The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1115-1125) copyright 2000.

Figure was selected by the author.